Starting phenix.real_space_refine on Sat Sep 28 20:24:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5b_22048/09_2024/6x5b_22048.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5b_22048/09_2024/6x5b_22048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5b_22048/09_2024/6x5b_22048.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5b_22048/09_2024/6x5b_22048.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5b_22048/09_2024/6x5b_22048.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5b_22048/09_2024/6x5b_22048.cif" } resolution = 3.6 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= 0.004 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: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 12723 2.51 5 N 3456 2.21 5 O 3945 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 20232 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2769 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 21, 'TRANS': 331} Chain breaks: 5 Chain: "B" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1184 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 2, 'TRANS': 146} Chain: "C" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 768 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "F" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 812 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "I" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 971 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'UOV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: G, N, D, J, E, K, H, O, M, L, R, T, S, U Time building chain proxies: 9.61, per 1000 atoms: 0.47 Number of scatterers: 20232 At special positions: 0 Unit cell: (150.65, 156.4, 140.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 3945 8.00 N 3456 7.00 C 12723 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.08 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.07 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 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 Links applied ALPHA1-2 " MAN Q 4 " - " MAN Q 5 " " MAN S 4 " - " MAN S 5 " " MAN U 4 " - " MAN U 5 " ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " NAG-ASN " NAG A 607 " - " ASN A 276 " " NAG A 608 " - " ASN A 295 " " NAG A 609 " - " ASN A 332 " " NAG A 610 " - " ASN A 362 " " NAG A 611 " - " ASN A 386 " " NAG A 612 " - " ASN A 392 " " NAG A 613 " - " ASN A 413 " " NAG A 614 " - " ASN A 448 " " NAG B 701 " - " ASN B 611 " " NAG D 607 " - " ASN D 276 " " NAG D 608 " - " ASN D 295 " " NAG D 609 " - " ASN D 332 " " NAG D 610 " - " ASN D 362 " " NAG D 611 " - " ASN D 386 " " NAG D 612 " - " ASN D 392 " " NAG D 613 " - " ASN D 413 " " NAG D 614 " - " ASN D 448 " " NAG E 701 " - " ASN E 611 " " NAG J 607 " - " ASN J 276 " " NAG J 608 " - " ASN J 295 " " NAG J 609 " - " ASN J 332 " " NAG J 610 " - " ASN J 362 " " NAG J 611 " - " ASN J 386 " " NAG J 612 " - " ASN J 392 " " NAG J 613 " - " ASN J 413 " " NAG J 614 " - " ASN J 448 " " NAG K 701 " - " ASN K 611 " " NAG P 1 " - " ASN A 241 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN D 241 " " NAG S 1 " - " ASN D 262 " " NAG T 1 " - " ASN J 241 " " NAG U 1 " - " ASN J 262 " Time building additional restraints: 5.90 Conformation dependent library (CDL) restraints added in 2.7 seconds 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4614 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 45 sheets defined 24.0% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.58 Creating SS restraints... Processing helix chain 'A' and resid 65 through 68 Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 99 through 114 Processing helix chain 'A' and resid 334 through 353 removed outlier: 3.730A pdb=" N GLU A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.929A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 524 removed outlier: 3.843A pdb=" N PHE B 522 " --> pdb=" O PHE B 518 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY B 524 " --> pdb=" O LEU B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 528 Processing helix chain 'B' and resid 529 through 546 Processing helix chain 'B' and resid 561 through 564 Processing helix chain 'B' and resid 565 through 593 removed outlier: 3.995A pdb=" N TRP B 571 " --> pdb=" O GLN B 567 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN B 591 " --> pdb=" O LEU B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 597 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.703A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 removed outlier: 4.142A pdb=" N LYS B 633 " --> pdb=" O MET B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 658 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'C' and resid 58 through 64 removed outlier: 4.461A pdb=" N ASP C 63 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 79 Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 99 through 100C Processing helix chain 'D' and resid 65 through 68 Processing helix chain 'D' and resid 69 through 74 Processing helix chain 'D' and resid 99 through 114 Processing helix chain 'D' and resid 334 through 353 removed outlier: 3.729A pdb=" N GLU D 351 " --> pdb=" O ALA D 347 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN D 352 " --> pdb=" O LYS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 475 through 484 removed outlier: 3.929A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 516 through 524 removed outlier: 3.843A pdb=" N PHE E 522 " --> pdb=" O PHE E 518 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 528 Processing helix chain 'E' and resid 529 through 546 Processing helix chain 'E' and resid 561 through 564 Processing helix chain 'E' and resid 565 through 593 removed outlier: 3.995A pdb=" N TRP E 571 " --> pdb=" O GLN E 567 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN E 591 " --> pdb=" O LEU E 587 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 597 Processing helix chain 'E' and resid 618 through 626 removed outlier: 3.702A pdb=" N MET E 626 " --> pdb=" O ILE E 622 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 635 removed outlier: 4.142A pdb=" N LYS E 633 " --> pdb=" O MET E 629 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 658 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'G' and resid 58 through 64 removed outlier: 4.461A pdb=" N ASP G 63 " --> pdb=" O SER G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 79 Processing helix chain 'I' and resid 28 through 30 No H-bonds generated for 'chain 'I' and resid 28 through 30' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'I' and resid 99 through 100C Processing helix chain 'J' and resid 65 through 68 Processing helix chain 'J' and resid 69 through 74 Processing helix chain 'J' and resid 99 through 114 Processing helix chain 'J' and resid 334 through 353 removed outlier: 3.729A pdb=" N GLU J 351 " --> pdb=" O ALA J 347 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN J 352 " --> pdb=" O LYS J 348 " (cutoff:3.500A) Processing helix chain 'J' and resid 368 through 373 Processing helix chain 'J' and resid 475 through 484 removed outlier: 3.928A pdb=" N GLU J 482 " --> pdb=" O ASN J 478 " (cutoff:3.500A) Processing helix chain 'K' and resid 516 through 524 removed outlier: 3.843A pdb=" N PHE K 522 " --> pdb=" O PHE K 518 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY K 524 " --> pdb=" O LEU K 520 " (cutoff:3.500A) Processing helix chain 'K' and resid 525 through 528 Processing helix chain 'K' and resid 529 through 546 Processing helix chain 'K' and resid 561 through 564 Processing helix chain 'K' and resid 565 through 593 removed outlier: 3.995A pdb=" N TRP K 571 " --> pdb=" O GLN K 567 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN K 591 " --> pdb=" O LEU K 587 " (cutoff:3.500A) Processing helix chain 'K' and resid 594 through 597 Processing helix chain 'K' and resid 618 through 626 removed outlier: 3.703A pdb=" N MET K 626 " --> pdb=" O ILE K 622 " (cutoff:3.500A) Processing helix chain 'K' and resid 627 through 635 removed outlier: 4.142A pdb=" N LYS K 633 " --> pdb=" O MET K 629 " (cutoff:3.500A) Processing helix chain 'K' and resid 638 through 658 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'N' and resid 58 through 64 removed outlier: 4.462A pdb=" N ASP N 63 " --> pdb=" O SER N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 79 Processing helix chain 'O' and resid 28 through 30 No H-bonds generated for 'chain 'O' and resid 28 through 30' Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'O' and resid 99 through 100C Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.337A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 199 through 202 Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.643A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 9.957A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.476A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.399A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.002A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.838A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.002A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.399A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.476A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.957A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA9, first strand: chain 'L' and resid 45 through 49 removed outlier: 6.656A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 45 through 49 removed outlier: 6.656A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 2 through 5 removed outlier: 4.767A pdb=" N PHE C 26 " --> pdb=" O ASN C 39 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 37 " --> pdb=" O TRP C 28 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ASN C 30 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LYS C 35 " --> pdb=" O ASN C 30 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY C 38 " --> pdb=" O THR C 45 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 12 through 17 Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.270A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL H 56 " --> pdb=" O ILE H 52 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.270A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.337A pdb=" N VAL E 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL D 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N THR E 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N TYR D 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N CYS E 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AB9, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AC1, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'D' and resid 199 through 202 Processing sheet with id=AC3, first strand: chain 'D' and resid 259 through 261 removed outlier: 3.643A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 9.957A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.476A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N SER D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.399A pdb=" N VAL D 292 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.002A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 271 through 273 removed outlier: 6.838A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 10.002A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.399A pdb=" N VAL D 292 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N SER D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.476A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.957A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AC6, first strand: chain 'F' and resid 45 through 49 removed outlier: 6.657A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 45 through 49 removed outlier: 6.657A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 2 through 5 removed outlier: 4.767A pdb=" N PHE G 26 " --> pdb=" O ASN G 39 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU G 37 " --> pdb=" O TRP G 28 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ASN G 30 " --> pdb=" O LYS G 35 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LYS G 35 " --> pdb=" O ASN G 30 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY G 38 " --> pdb=" O THR G 45 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 12 through 17 Processing sheet with id=AD1, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.270A pdb=" N GLU I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL I 56 " --> pdb=" O ILE I 52 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.270A pdb=" N GLU I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 494 through 499 removed outlier: 5.337A pdb=" N VAL K 608 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL J 38 " --> pdb=" O THR K 606 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N THR K 606 " --> pdb=" O VAL J 38 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N TYR J 40 " --> pdb=" O CYS K 604 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N CYS K 604 " --> pdb=" O TYR J 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 45 through 47 Processing sheet with id=AD6, first strand: chain 'J' and resid 53 through 56 Processing sheet with id=AD7, first strand: chain 'J' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'J' and resid 199 through 202 Processing sheet with id=AD9, first strand: chain 'J' and resid 259 through 261 removed outlier: 3.642A pdb=" N GLY J 451 " --> pdb=" O LEU J 260 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ARG J 444 " --> pdb=" O ILE J 294 " (cutoff:3.500A) removed outlier: 11.476A pdb=" N ILE J 294 " --> pdb=" O ARG J 444 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N SER J 446 " --> pdb=" O VAL J 292 " (cutoff:3.500A) removed outlier: 10.399A pdb=" N VAL J 292 " --> pdb=" O SER J 446 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N ASN J 448 " --> pdb=" O GLU J 290 " (cutoff:3.500A) removed outlier: 10.002A pdb=" N GLU J 290 " --> pdb=" O ASN J 448 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR J 450 " --> pdb=" O LEU J 288 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE J 382 " --> pdb=" O LYS J 421 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 271 through 273 removed outlier: 6.838A pdb=" N THR J 450 " --> pdb=" O LEU J 288 " (cutoff:3.500A) removed outlier: 10.002A pdb=" N GLU J 290 " --> pdb=" O ASN J 448 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N ASN J 448 " --> pdb=" O GLU J 290 " (cutoff:3.500A) removed outlier: 10.399A pdb=" N VAL J 292 " --> pdb=" O SER J 446 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N SER J 446 " --> pdb=" O VAL J 292 " (cutoff:3.500A) removed outlier: 11.476A pdb=" N ILE J 294 " --> pdb=" O ARG J 444 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ARG J 444 " --> pdb=" O ILE J 294 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AE3, first strand: chain 'M' and resid 45 through 49 removed outlier: 6.657A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 45 through 49 removed outlier: 6.657A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 2 through 5 removed outlier: 4.766A pdb=" N PHE N 26 " --> pdb=" O ASN N 39 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU N 37 " --> pdb=" O TRP N 28 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ASN N 30 " --> pdb=" O LYS N 35 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LYS N 35 " --> pdb=" O ASN N 30 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY N 38 " --> pdb=" O THR N 45 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 12 through 17 Processing sheet with id=AE7, first strand: chain 'O' and resid 3 through 6 Processing sheet with id=AE8, first strand: chain 'O' and resid 10 through 11 removed outlier: 6.270A pdb=" N GLU O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL O 56 " --> pdb=" O ILE O 52 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 10 through 11 removed outlier: 6.270A pdb=" N GLU O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) 861 hydrogen bonds defined for protein. 2142 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: 7.88 Time building geometry restraints manager: 6.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3689 1.31 - 1.45: 6397 1.45 - 1.59: 10290 1.59 - 1.73: 120 1.73 - 1.86: 141 Bond restraints: 20637 Sorted by residual: bond pdb=" NE ARG A 504 " pdb=" CZ ARG A 504 " ideal model delta sigma weight residual 1.326 1.402 -0.076 1.10e-02 8.26e+03 4.82e+01 bond pdb=" NE ARG D 504 " pdb=" CZ ARG D 504 " ideal model delta sigma weight residual 1.326 1.402 -0.076 1.10e-02 8.26e+03 4.77e+01 bond pdb=" NE ARG J 504 " pdb=" CZ ARG J 504 " ideal model delta sigma weight residual 1.326 1.402 -0.076 1.10e-02 8.26e+03 4.74e+01 bond pdb=" CG HIS D 374 " pdb=" CD2 HIS D 374 " ideal model delta sigma weight residual 1.354 1.283 0.071 1.10e-02 8.26e+03 4.15e+01 bond pdb=" CG HIS A 374 " pdb=" CD2 HIS A 374 " ideal model delta sigma weight residual 1.354 1.283 0.071 1.10e-02 8.26e+03 4.11e+01 ... (remaining 20632 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 24488 2.56 - 5.13: 3072 5.13 - 7.69: 411 7.69 - 10.25: 13 10.25 - 12.81: 12 Bond angle restraints: 27996 Sorted by residual: angle pdb=" C PRO A 437 " pdb=" N PRO A 438 " pdb=" CA PRO A 438 " ideal model delta sigma weight residual 119.78 127.40 -7.62 1.03e+00 9.43e-01 5.47e+01 angle pdb=" C PRO J 437 " pdb=" N PRO J 438 " pdb=" CA PRO J 438 " ideal model delta sigma weight residual 119.78 127.38 -7.60 1.03e+00 9.43e-01 5.44e+01 angle pdb=" N VAL J 65 " pdb=" CA VAL J 65 " pdb=" C VAL J 65 " ideal model delta sigma weight residual 110.42 117.48 -7.06 9.60e-01 1.09e+00 5.41e+01 angle pdb=" C PRO D 437 " pdb=" N PRO D 438 " pdb=" CA PRO D 438 " ideal model delta sigma weight residual 119.78 127.35 -7.57 1.03e+00 9.43e-01 5.41e+01 angle pdb=" N VAL A 65 " pdb=" CA VAL A 65 " pdb=" C VAL A 65 " ideal model delta sigma weight residual 110.42 117.47 -7.05 9.60e-01 1.09e+00 5.39e+01 ... (remaining 27991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.73: 12593 21.73 - 43.47: 239 43.47 - 65.20: 90 65.20 - 86.93: 23 86.93 - 108.66: 12 Dihedral angle restraints: 12957 sinusoidal: 5814 harmonic: 7143 Sorted by residual: dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -166.17 80.17 1 1.00e+01 1.00e-02 7.96e+01 dihedral pdb=" CA CYS A 119 " pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " ideal model delta sinusoidal sigma weight residual -73.00 -3.86 -69.14 1 2.00e+01 2.50e-03 1.55e+01 dihedral pdb=" O4 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C5 BMA Q 3 " pdb=" O5 BMA Q 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.95 108.66 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 12954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2230 0.104 - 0.207: 757 0.207 - 0.311: 142 0.311 - 0.414: 90 0.414 - 0.518: 42 Chirality restraints: 3261 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.25e+02 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.23e+02 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.22e+02 ... (remaining 3258 not shown) Planarity restraints: 3552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN K 611 " -0.095 2.00e-02 2.50e+03 9.97e-02 1.24e+02 pdb=" CG ASN K 611 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN K 611 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN K 611 " 0.155 2.00e-02 2.50e+03 pdb=" C1 NAG K 701 " -0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 611 " -0.095 2.00e-02 2.50e+03 9.97e-02 1.24e+02 pdb=" CG ASN E 611 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN E 611 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN E 611 " 0.155 2.00e-02 2.50e+03 pdb=" C1 NAG E 701 " -0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 611 " -0.095 2.00e-02 2.50e+03 9.96e-02 1.24e+02 pdb=" CG ASN B 611 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN B 611 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN B 611 " 0.155 2.00e-02 2.50e+03 pdb=" C1 NAG B 701 " -0.121 2.00e-02 2.50e+03 ... (remaining 3549 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 123 2.59 - 3.17: 16932 3.17 - 3.75: 30287 3.75 - 4.32: 45797 4.32 - 4.90: 72047 Nonbonded interactions: 165186 Sorted by model distance: nonbonded pdb=" SG CYS G 16 " pdb=" SG CYS G 84 " model vdw 2.017 3.760 nonbonded pdb=" SG CYS N 16 " pdb=" SG CYS N 84 " model vdw 2.017 3.760 nonbonded pdb=" SG CYS C 16 " pdb=" SG CYS C 84 " model vdw 2.017 3.760 nonbonded pdb=" SG CYS E 598 " pdb=" SG CYS E 604 " model vdw 2.021 3.760 nonbonded pdb=" SG CYS K 598 " pdb=" SG CYS K 604 " model vdw 2.022 3.760 ... (remaining 165181 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 'D' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'N' } ncs_group { reference = chain 'F' selection = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'Q' selection = chain 'S' selection = chain 'U' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 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: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 48.680 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 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 : 0.021 0.122 20637 Z= 1.385 Angle : 1.746 12.814 27996 Z= 1.136 Chirality : 0.126 0.518 3261 Planarity : 0.009 0.055 3519 Dihedral : 11.149 108.664 8316 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.48 (0.17), residues: 2427 helix: -0.36 (0.22), residues: 444 sheet: 0.77 (0.20), residues: 687 loop : 0.48 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.010 TRP N 28 HIS 0.008 0.002 HIS J 374 PHE 0.029 0.007 PHE K 522 TYR 0.068 0.010 TYR F 91 ARG 0.006 0.001 ARG G 59 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 700 time to evaluate : 2.474 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 428 GLN cc_start: 0.7463 (mp10) cc_final: 0.6898 (mt0) REVERT: A 446 SER cc_start: 0.8579 (m) cc_final: 0.8068 (p) REVERT: A 475 MET cc_start: 0.7946 (mmp) cc_final: 0.7640 (tpp) REVERT: B 638 TYR cc_start: 0.7099 (m-80) cc_final: 0.6885 (m-10) REVERT: L 52 SER cc_start: 0.7491 (p) cc_final: 0.7282 (t) REVERT: C 74 LEU cc_start: 0.7327 (tp) cc_final: 0.6422 (tp) REVERT: H 81 GLU cc_start: 0.6204 (tt0) cc_final: 0.5926 (tt0) REVERT: H 111 VAL cc_start: 0.5893 (t) cc_final: 0.5347 (t) REVERT: D 446 SER cc_start: 0.8450 (m) cc_final: 0.7985 (p) REVERT: E 638 TYR cc_start: 0.6894 (m-80) cc_final: 0.6657 (m-10) REVERT: G 60 SER cc_start: 0.9055 (p) cc_final: 0.8830 (p) REVERT: G 74 LEU cc_start: 0.7418 (tp) cc_final: 0.6622 (tp) REVERT: G 86 VAL cc_start: 0.8044 (t) cc_final: 0.7637 (t) REVERT: I 12 LYS cc_start: 0.7676 (mmtt) cc_final: 0.7110 (mmtt) REVERT: I 36 TRP cc_start: 0.7482 (m100) cc_final: 0.7117 (m100) REVERT: I 111 VAL cc_start: 0.6246 (t) cc_final: 0.5462 (t) REVERT: J 116 LEU cc_start: 0.8745 (mt) cc_final: 0.8519 (mp) REVERT: J 428 GLN cc_start: 0.7638 (mp10) cc_final: 0.7174 (mt0) REVERT: J 446 SER cc_start: 0.8557 (m) cc_final: 0.8232 (p) REVERT: J 475 MET cc_start: 0.7925 (mmp) cc_final: 0.7708 (mmm) REVERT: J 482 GLU cc_start: 0.6800 (mm-30) cc_final: 0.6581 (mm-30) REVERT: K 627 THR cc_start: 0.8250 (p) cc_final: 0.7938 (p) REVERT: K 629 MET cc_start: 0.7935 (mmm) cc_final: 0.7626 (mmm) REVERT: K 638 TYR cc_start: 0.6863 (m-80) cc_final: 0.6572 (m-10) REVERT: O 108 LEU cc_start: 0.8688 (tp) cc_final: 0.8471 (tt) REVERT: O 111 VAL cc_start: 0.6308 (t) cc_final: 0.5383 (t) outliers start: 0 outliers final: 0 residues processed: 700 average time/residue: 0.3334 time to fit residues: 349.0752 Evaluate side-chains 362 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 362 time to evaluate : 2.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.7980 chunk 181 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 188 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 HIS A 355 ASN A 363 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN L 93 ASN C 33 GLN C 94 GLN H 58 HIS H 62 HIS D 72 HIS ** D 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 GLN D 229 ASN D 249 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 428 GLN E 554 ASN E 607 ASN E 620 ASN F 93 ASN G 25 GLN I 58 HIS ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 249 HIS J 363 HIS ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 564 HIS K 620 ASN M 93 ASN O 58 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 20637 Z= 0.254 Angle : 0.741 11.752 27996 Z= 0.389 Chirality : 0.049 0.204 3261 Planarity : 0.005 0.047 3519 Dihedral : 7.654 68.922 3678 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.28 % Allowed : 10.10 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.53 (0.17), residues: 2427 helix: 0.87 (0.25), residues: 441 sheet: 0.83 (0.21), residues: 621 loop : 0.04 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 94 HIS 0.009 0.002 HIS A 66 PHE 0.020 0.002 PHE D 53 TYR 0.027 0.003 TYR A 435 ARG 0.007 0.001 ARG I 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 426 time to evaluate : 2.397 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: A 64 GLU cc_start: 0.7783 (tm-30) cc_final: 0.6727 (tt0) REVERT: A 426 MET cc_start: 0.7652 (mtp) cc_final: 0.7398 (mtp) REVERT: A 428 GLN cc_start: 0.7850 (mp10) cc_final: 0.7215 (mt0) REVERT: A 446 SER cc_start: 0.8557 (m) cc_final: 0.7983 (p) REVERT: L 2 LEU cc_start: 0.4991 (OUTLIER) cc_final: 0.4514 (mt) REVERT: H 3 GLN cc_start: 0.8450 (pm20) cc_final: 0.8222 (pm20) REVERT: H 19 LYS cc_start: 0.6834 (tptm) cc_final: 0.6107 (tptp) REVERT: D 64 GLU cc_start: 0.7728 (tm-30) cc_final: 0.6772 (tt0) REVERT: D 475 MET cc_start: 0.7877 (mmm) cc_final: 0.7247 (mmm) REVERT: E 565 MET cc_start: 0.7127 (ptm) cc_final: 0.6846 (ptm) REVERT: E 629 MET cc_start: 0.7671 (mmm) cc_final: 0.7459 (mmm) REVERT: G 86 VAL cc_start: 0.8382 (t) cc_final: 0.8080 (t) REVERT: I 52 ILE cc_start: 0.8091 (mm) cc_final: 0.7883 (mp) REVERT: J 64 GLU cc_start: 0.7559 (tm-30) cc_final: 0.6708 (tt0) REVERT: J 428 GLN cc_start: 0.7763 (mp10) cc_final: 0.7168 (mt0) REVERT: J 446 SER cc_start: 0.8617 (m) cc_final: 0.8117 (p) REVERT: J 482 GLU cc_start: 0.6706 (mm-30) cc_final: 0.6493 (mm-30) REVERT: M 2 LEU cc_start: 0.4371 (OUTLIER) cc_final: 0.3720 (mt) REVERT: M 24 ARG cc_start: 0.6739 (ttm110) cc_final: 0.6467 (ttm-80) REVERT: O 12 LYS cc_start: 0.6707 (mptt) cc_final: 0.5275 (mttp) REVERT: O 19 LYS cc_start: 0.6706 (tttm) cc_final: 0.5975 (tptm) outliers start: 49 outliers final: 19 residues processed: 454 average time/residue: 0.3191 time to fit residues: 220.7914 Evaluate side-chains 338 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 317 time to evaluate : 2.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain E residue 564 HIS Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain K residue 563 GLN Chi-restraints excluded: chain K residue 646 LEU Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 54 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 218 optimal weight: 4.9990 chunk 235 optimal weight: 9.9990 chunk 194 optimal weight: 2.9990 chunk 216 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN C 52 ASN H 82BASN D 80 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 607 ASN E 658 GLN F 42 GLN ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 ASN J 363 HIS ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 417 GLN ** K 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 620 ASN ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 20637 Z= 0.395 Angle : 0.775 9.102 27996 Z= 0.402 Chirality : 0.051 0.184 3261 Planarity : 0.005 0.058 3519 Dihedral : 6.425 40.721 3678 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.45 % Allowed : 12.66 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.17), residues: 2427 helix: 0.70 (0.25), residues: 441 sheet: 0.69 (0.22), residues: 618 loop : -0.61 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP H 36 HIS 0.007 0.002 HIS D 363 PHE 0.023 0.003 PHE J 383 TYR 0.025 0.003 TYR H 100E ARG 0.006 0.001 ARG I 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 375 time to evaluate : 2.336 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: A 64 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7003 (tt0) REVERT: C 94 GLN cc_start: 0.7069 (tp-100) cc_final: 0.6306 (tp-100) REVERT: H 3 GLN cc_start: 0.8480 (pm20) cc_final: 0.8259 (pm20) REVERT: D 64 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7077 (tt0) REVERT: I 19 LYS cc_start: 0.7323 (OUTLIER) cc_final: 0.6880 (tmtt) REVERT: I 91 PHE cc_start: 0.6616 (OUTLIER) cc_final: 0.5585 (p90) REVERT: J 64 GLU cc_start: 0.7860 (tm-30) cc_final: 0.6924 (tt0) REVERT: O 105 GLN cc_start: 0.7917 (mp10) cc_final: 0.7670 (pp30) outliers start: 74 outliers final: 48 residues processed: 417 average time/residue: 0.3135 time to fit residues: 204.7134 Evaluate side-chains 351 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 301 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 485 LYS Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 564 HIS Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain K residue 563 GLN Chi-restraints excluded: chain K residue 564 HIS Chi-restraints excluded: chain K residue 565 MET Chi-restraints excluded: chain K residue 618 THR Chi-restraints excluded: chain K residue 646 LEU Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 79 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 30.0000 chunk 164 optimal weight: 0.0870 chunk 113 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 146 optimal weight: 9.9990 chunk 219 optimal weight: 0.0060 chunk 231 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 overall best weight: 0.7978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 80 ASN A 363 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 653 GLN F 42 GLN F 93 ASN J 80 ASN J 363 HIS ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 93 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20637 Z= 0.203 Angle : 0.635 8.289 27996 Z= 0.331 Chirality : 0.046 0.176 3261 Planarity : 0.005 0.060 3519 Dihedral : 5.598 30.571 3678 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.98 % Allowed : 14.62 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.04 (0.17), residues: 2427 helix: 1.01 (0.25), residues: 441 sheet: 0.69 (0.22), residues: 588 loop : -0.68 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 36 HIS 0.007 0.001 HIS J 66 PHE 0.018 0.002 PHE J 53 TYR 0.034 0.002 TYR M 49 ARG 0.005 0.000 ARG H 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 361 time to evaluate : 2.160 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: A 446 SER cc_start: 0.8756 (m) cc_final: 0.8140 (p) REVERT: C 94 GLN cc_start: 0.7014 (tp-100) cc_final: 0.6319 (tp-100) REVERT: D 64 GLU cc_start: 0.7983 (tm-30) cc_final: 0.6862 (tt0) REVERT: D 418 CYS cc_start: 0.8052 (m) cc_final: 0.7802 (m) REVERT: E 567 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7512 (tp40) REVERT: I 19 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7284 (tmtt) REVERT: I 91 PHE cc_start: 0.6573 (OUTLIER) cc_final: 0.5476 (p90) REVERT: J 64 GLU cc_start: 0.7798 (tm-30) cc_final: 0.6814 (tt0) REVERT: J 65 VAL cc_start: 0.7256 (OUTLIER) cc_final: 0.6865 (t) REVERT: J 82 GLN cc_start: 0.7191 (mm-40) cc_final: 0.6951 (mm-40) REVERT: J 446 SER cc_start: 0.8737 (m) cc_final: 0.8304 (p) REVERT: K 565 MET cc_start: 0.7155 (ptm) cc_final: 0.6605 (ttp) REVERT: K 657 GLU cc_start: 0.7565 (tt0) cc_final: 0.7319 (tt0) REVERT: M 24 ARG cc_start: 0.6690 (ttm110) cc_final: 0.6323 (ttm-80) REVERT: O 72 ASP cc_start: 0.7254 (t0) cc_final: 0.6944 (t0) REVERT: O 91 PHE cc_start: 0.6030 (OUTLIER) cc_final: 0.5511 (p90) outliers start: 64 outliers final: 29 residues processed: 390 average time/residue: 0.2824 time to fit residues: 174.8361 Evaluate side-chains 338 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 304 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 485 LYS Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 567 GLN Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 80 ASN Chi-restraints excluded: chain J residue 439 ILE Chi-restraints excluded: chain K residue 618 THR Chi-restraints excluded: chain K residue 646 LEU Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 91 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 197 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 118 optimal weight: 0.0370 chunk 208 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS A 229 ASN A 325 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 GLN E 658 GLN F 42 GLN ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 229 ASN J 363 HIS J 374 HIS J 377 ASN ** K 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 GLN ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20637 Z= 0.357 Angle : 0.699 9.323 27996 Z= 0.363 Chirality : 0.048 0.201 3261 Planarity : 0.005 0.051 3519 Dihedral : 5.653 36.454 3678 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.72 % Allowed : 14.85 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.22 (0.17), residues: 2427 helix: 0.92 (0.25), residues: 441 sheet: 0.80 (0.23), residues: 552 loop : -0.89 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP H 36 HIS 0.006 0.001 HIS D 363 PHE 0.024 0.002 PHE A 53 TYR 0.031 0.003 TYR M 49 ARG 0.007 0.001 ARG H 31 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 329 time to evaluate : 2.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.6689 (p0) cc_final: 0.5997 (p0) REVERT: A 100 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.7244 (mtp) REVERT: B 629 MET cc_start: 0.7814 (mmm) cc_final: 0.7610 (mmm) REVERT: C 80 ASP cc_start: 0.5494 (m-30) cc_final: 0.4860 (t70) REVERT: C 94 GLN cc_start: 0.7243 (tp-100) cc_final: 0.6659 (tp-100) REVERT: H 39 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.6684 (tp-100) REVERT: H 91 PHE cc_start: 0.6795 (OUTLIER) cc_final: 0.5878 (p90) REVERT: D 64 GLU cc_start: 0.8000 (tm-30) cc_final: 0.6951 (tt0) REVERT: D 80 ASN cc_start: 0.6840 (p0) cc_final: 0.6631 (p0) REVERT: D 418 CYS cc_start: 0.8138 (m) cc_final: 0.7906 (m) REVERT: G 80 ASP cc_start: 0.5939 (m-30) cc_final: 0.5453 (t0) REVERT: I 19 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7399 (tmtt) REVERT: I 91 PHE cc_start: 0.6804 (OUTLIER) cc_final: 0.5780 (p90) REVERT: J 64 GLU cc_start: 0.7950 (tm-30) cc_final: 0.6900 (tt0) REVERT: J 65 VAL cc_start: 0.7352 (OUTLIER) cc_final: 0.7041 (t) REVERT: J 80 ASN cc_start: 0.6456 (p0) cc_final: 0.6250 (p0) REVERT: K 565 MET cc_start: 0.7231 (ptm) cc_final: 0.6732 (ttp) REVERT: K 629 MET cc_start: 0.7883 (mmm) cc_final: 0.7527 (mmm) REVERT: K 657 GLU cc_start: 0.7718 (tt0) cc_final: 0.7468 (tt0) REVERT: M 24 ARG cc_start: 0.6817 (ttm110) cc_final: 0.6451 (ttm-80) REVERT: O 72 ASP cc_start: 0.7332 (t0) cc_final: 0.7029 (t0) REVERT: O 91 PHE cc_start: 0.6359 (OUTLIER) cc_final: 0.5831 (p90) outliers start: 80 outliers final: 54 residues processed: 377 average time/residue: 0.2832 time to fit residues: 170.6725 Evaluate side-chains 359 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 298 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 216 HIS Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 485 LYS Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 564 HIS Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 644 THR Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 216 HIS Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain J residue 439 ILE Chi-restraints excluded: chain K residue 564 HIS Chi-restraints excluded: chain K residue 618 THR Chi-restraints excluded: chain K residue 646 LEU Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 91 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.9990 chunk 208 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 232 optimal weight: 9.9990 chunk 192 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 363 HIS K 658 GLN ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20637 Z= 0.202 Angle : 0.622 10.635 27996 Z= 0.322 Chirality : 0.046 0.172 3261 Planarity : 0.005 0.055 3519 Dihedral : 5.305 33.998 3678 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.07 % Allowed : 16.11 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.15 (0.17), residues: 2427 helix: 1.18 (0.26), residues: 441 sheet: 0.67 (0.22), residues: 612 loop : -0.90 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP H 36 HIS 0.006 0.001 HIS J 66 PHE 0.018 0.002 PHE J 53 TYR 0.036 0.002 TYR M 49 ARG 0.005 0.000 ARG H 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 358 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 80 ASP cc_start: 0.5327 (m-30) cc_final: 0.4703 (t0) REVERT: C 94 GLN cc_start: 0.7158 (tp-100) cc_final: 0.6640 (tp-100) REVERT: H 39 GLN cc_start: 0.7288 (OUTLIER) cc_final: 0.6744 (tp-100) REVERT: H 91 PHE cc_start: 0.6711 (OUTLIER) cc_final: 0.5834 (p90) REVERT: D 64 GLU cc_start: 0.7927 (tm-30) cc_final: 0.6784 (tt0) REVERT: D 80 ASN cc_start: 0.6358 (p0) cc_final: 0.6063 (p0) REVERT: D 328 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7885 (tp-100) REVERT: D 372 VAL cc_start: 0.7989 (t) cc_final: 0.7782 (p) REVERT: E 567 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7361 (tp40) REVERT: G 54 ARG cc_start: 0.8507 (mtp180) cc_final: 0.8201 (mtp180) REVERT: G 80 ASP cc_start: 0.5893 (m-30) cc_final: 0.5470 (t0) REVERT: I 19 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7637 (tmtt) REVERT: I 91 PHE cc_start: 0.6672 (OUTLIER) cc_final: 0.5540 (p90) REVERT: J 64 GLU cc_start: 0.7848 (tm-30) cc_final: 0.6810 (tt0) REVERT: J 65 VAL cc_start: 0.7355 (OUTLIER) cc_final: 0.6988 (t) REVERT: J 80 ASN cc_start: 0.6151 (p0) cc_final: 0.5924 (p0) REVERT: J 446 SER cc_start: 0.8783 (m) cc_final: 0.8288 (p) REVERT: K 565 MET cc_start: 0.7124 (ptm) cc_final: 0.6678 (ttp) REVERT: K 629 MET cc_start: 0.7676 (mmm) cc_final: 0.7307 (mmm) REVERT: K 657 GLU cc_start: 0.7573 (tt0) cc_final: 0.7356 (tt0) REVERT: M 70 GLU cc_start: 0.6141 (mm-30) cc_final: 0.5886 (mp0) REVERT: O 72 ASP cc_start: 0.7377 (t0) cc_final: 0.7120 (t0) outliers start: 66 outliers final: 42 residues processed: 392 average time/residue: 0.2855 time to fit residues: 178.1549 Evaluate side-chains 372 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 323 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 216 HIS Chi-restraints excluded: chain D residue 328 GLN Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 564 HIS Chi-restraints excluded: chain E residue 567 GLN Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 216 HIS Chi-restraints excluded: chain J residue 439 ILE Chi-restraints excluded: chain K residue 564 HIS Chi-restraints excluded: chain K residue 618 THR Chi-restraints excluded: chain K residue 646 LEU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 10 GLU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 91 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 169 optimal weight: 0.0270 chunk 131 optimal weight: 20.0000 chunk 195 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 144 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN ** D 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 363 HIS ** K 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 93 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20637 Z= 0.245 Angle : 0.643 9.182 27996 Z= 0.331 Chirality : 0.046 0.162 3261 Planarity : 0.005 0.047 3519 Dihedral : 5.272 35.933 3678 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.40 % Allowed : 16.29 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.21 (0.17), residues: 2427 helix: 1.16 (0.25), residues: 441 sheet: 0.64 (0.22), residues: 612 loop : -0.97 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP O 36 HIS 0.004 0.001 HIS J 66 PHE 0.018 0.002 PHE A 53 TYR 0.048 0.002 TYR M 91 ARG 0.007 0.000 ARG N 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 333 time to evaluate : 2.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.6621 (OUTLIER) cc_final: 0.6389 (p0) REVERT: A 270 ILE cc_start: 0.8029 (mp) cc_final: 0.7650 (mt) REVERT: C 80 ASP cc_start: 0.5313 (m-30) cc_final: 0.4713 (t0) REVERT: C 94 GLN cc_start: 0.7135 (tp-100) cc_final: 0.6667 (tp-100) REVERT: H 39 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.6775 (tp-100) REVERT: H 91 PHE cc_start: 0.6700 (OUTLIER) cc_final: 0.5825 (p90) REVERT: D 64 GLU cc_start: 0.7826 (tm-30) cc_final: 0.6648 (tt0) REVERT: D 80 ASN cc_start: 0.6635 (p0) cc_final: 0.6336 (p0) REVERT: D 372 VAL cc_start: 0.8180 (t) cc_final: 0.7972 (p) REVERT: D 446 SER cc_start: 0.8809 (m) cc_final: 0.8249 (p) REVERT: E 567 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7460 (tp40) REVERT: I 19 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7686 (tmtt) REVERT: I 91 PHE cc_start: 0.6662 (OUTLIER) cc_final: 0.5665 (p90) REVERT: J 64 GLU cc_start: 0.7830 (tm-30) cc_final: 0.6763 (tt0) REVERT: J 65 VAL cc_start: 0.7261 (OUTLIER) cc_final: 0.6965 (t) REVERT: J 80 ASN cc_start: 0.6329 (p0) cc_final: 0.6111 (p0) REVERT: J 82 GLN cc_start: 0.7686 (tp40) cc_final: 0.7327 (tp40) REVERT: K 565 MET cc_start: 0.7084 (ptm) cc_final: 0.6655 (ttp) REVERT: K 629 MET cc_start: 0.7809 (mmm) cc_final: 0.7428 (mmm) REVERT: K 657 GLU cc_start: 0.7643 (tt0) cc_final: 0.7349 (tt0) REVERT: O 81 GLU cc_start: 0.6278 (OUTLIER) cc_final: 0.6063 (mm-30) outliers start: 73 outliers final: 51 residues processed: 374 average time/residue: 0.2803 time to fit residues: 166.4136 Evaluate side-chains 366 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 307 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 216 HIS Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 564 HIS Chi-restraints excluded: chain E residue 567 GLN Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 216 HIS Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 439 ILE Chi-restraints excluded: chain K residue 540 GLN Chi-restraints excluded: chain K residue 564 HIS Chi-restraints excluded: chain K residue 618 THR Chi-restraints excluded: chain K residue 646 LEU Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 10 GLU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 81 GLU Chi-restraints excluded: chain O residue 91 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 chunk 69 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 157 optimal weight: 9.9990 chunk 114 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 363 HIS ** K 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.5474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20637 Z= 0.215 Angle : 0.621 9.259 27996 Z= 0.322 Chirality : 0.045 0.239 3261 Planarity : 0.005 0.058 3519 Dihedral : 5.159 35.537 3678 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.03 % Allowed : 17.23 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.20 (0.17), residues: 2427 helix: 1.30 (0.26), residues: 441 sheet: 0.65 (0.22), residues: 582 loop : -0.98 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP O 36 HIS 0.005 0.001 HIS J 66 PHE 0.014 0.001 PHE J 53 TYR 0.040 0.002 TYR M 91 ARG 0.007 0.000 ARG N 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 348 time to evaluate : 2.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.6507 (OUTLIER) cc_final: 0.5942 (p0) REVERT: A 270 ILE cc_start: 0.7983 (mp) cc_final: 0.7609 (mt) REVERT: C 80 ASP cc_start: 0.5104 (m-30) cc_final: 0.4674 (t0) REVERT: C 94 GLN cc_start: 0.7271 (tp-100) cc_final: 0.6781 (tp-100) REVERT: H 39 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.6766 (tp-100) REVERT: H 91 PHE cc_start: 0.6660 (OUTLIER) cc_final: 0.5809 (p90) REVERT: D 64 GLU cc_start: 0.7840 (tm-30) cc_final: 0.6643 (tt0) REVERT: D 80 ASN cc_start: 0.6558 (p0) cc_final: 0.6239 (p0) REVERT: D 328 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7884 (tp-100) REVERT: D 338 TRP cc_start: 0.7633 (t-100) cc_final: 0.7394 (t-100) REVERT: D 372 VAL cc_start: 0.8143 (t) cc_final: 0.7932 (p) REVERT: D 446 SER cc_start: 0.8752 (m) cc_final: 0.8211 (p) REVERT: E 567 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7394 (tp40) REVERT: F 70 GLU cc_start: 0.7017 (mp0) cc_final: 0.6668 (mp0) REVERT: I 19 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7795 (tmtt) REVERT: I 91 PHE cc_start: 0.6731 (OUTLIER) cc_final: 0.5669 (p90) REVERT: J 64 GLU cc_start: 0.7800 (tm-30) cc_final: 0.6734 (tt0) REVERT: J 65 VAL cc_start: 0.7295 (OUTLIER) cc_final: 0.6940 (t) REVERT: J 80 ASN cc_start: 0.6429 (p0) cc_final: 0.6222 (p0) REVERT: J 82 GLN cc_start: 0.7755 (tp40) cc_final: 0.7424 (tp40) REVERT: K 565 MET cc_start: 0.7114 (ptm) cc_final: 0.6725 (ttp) REVERT: K 629 MET cc_start: 0.7798 (mmm) cc_final: 0.7474 (mmm) REVERT: K 657 GLU cc_start: 0.7636 (tt0) cc_final: 0.7290 (tt0) REVERT: O 10 GLU cc_start: 0.6046 (OUTLIER) cc_final: 0.5745 (tm-30) outliers start: 65 outliers final: 47 residues processed: 385 average time/residue: 0.2849 time to fit residues: 172.8343 Evaluate side-chains 375 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 319 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 216 HIS Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 328 GLN Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 564 HIS Chi-restraints excluded: chain E residue 567 GLN Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 216 HIS Chi-restraints excluded: chain J residue 439 ILE Chi-restraints excluded: chain K residue 540 GLN Chi-restraints excluded: chain K residue 564 HIS Chi-restraints excluded: chain K residue 592 LEU Chi-restraints excluded: chain K residue 618 THR Chi-restraints excluded: chain K residue 645 LEU Chi-restraints excluded: chain K residue 646 LEU Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 10 GLU Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 91 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 9.9990 chunk 221 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 215 optimal weight: 30.0000 chunk 129 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 169 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 194 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 214 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 GLN ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 363 HIS ** K 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.5687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 20637 Z= 0.392 Angle : 0.743 8.816 27996 Z= 0.383 Chirality : 0.049 0.170 3261 Planarity : 0.005 0.067 3519 Dihedral : 5.726 41.613 3678 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.72 % Allowed : 17.04 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.56 (0.17), residues: 2427 helix: 1.05 (0.25), residues: 423 sheet: 0.43 (0.22), residues: 585 loop : -1.21 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP O 36 HIS 0.007 0.001 HIS A 216 PHE 0.017 0.002 PHE J 53 TYR 0.034 0.003 TYR F 91 ARG 0.005 0.000 ARG G 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 320 time to evaluate : 2.394 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7956 (tm-30) cc_final: 0.6678 (tt0) REVERT: A 270 ILE cc_start: 0.8088 (mp) cc_final: 0.7733 (mt) REVERT: C 80 ASP cc_start: 0.5130 (m-30) cc_final: 0.4847 (t0) REVERT: C 94 GLN cc_start: 0.7374 (tp-100) cc_final: 0.6977 (tp40) REVERT: H 39 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.6777 (tp-100) REVERT: H 91 PHE cc_start: 0.6911 (OUTLIER) cc_final: 0.5992 (p90) REVERT: D 328 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7820 (tp-100) REVERT: D 338 TRP cc_start: 0.7588 (t-100) cc_final: 0.7388 (t-100) REVERT: D 434 MET cc_start: 0.7871 (ttp) cc_final: 0.7458 (ttp) REVERT: E 567 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7675 (tp40) REVERT: I 19 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7891 (tmtt) REVERT: J 80 ASN cc_start: 0.6667 (p0) cc_final: 0.6379 (p0) REVERT: K 565 MET cc_start: 0.7263 (ptm) cc_final: 0.7016 (ttp) REVERT: K 629 MET cc_start: 0.7980 (mmm) cc_final: 0.7696 (mmm) REVERT: K 657 GLU cc_start: 0.7775 (tt0) cc_final: 0.7494 (tt0) REVERT: M 1 GLU cc_start: 0.6846 (mm-30) cc_final: 0.6612 (tm-30) REVERT: O 10 GLU cc_start: 0.6060 (OUTLIER) cc_final: 0.5779 (tm-30) outliers start: 80 outliers final: 64 residues processed: 373 average time/residue: 0.2932 time to fit residues: 174.1986 Evaluate side-chains 375 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 305 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 216 HIS Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 328 GLN Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 485 LYS Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 496 ILE Chi-restraints excluded: chain E residue 564 HIS Chi-restraints excluded: chain E residue 567 GLN Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain E residue 644 THR Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 216 HIS Chi-restraints excluded: chain J residue 228 CYS Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain J residue 439 ILE Chi-restraints excluded: chain J residue 496 ILE Chi-restraints excluded: chain K residue 540 GLN Chi-restraints excluded: chain K residue 564 HIS Chi-restraints excluded: chain K residue 592 LEU Chi-restraints excluded: chain K residue 618 THR Chi-restraints excluded: chain K residue 645 LEU Chi-restraints excluded: chain K residue 646 LEU Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 10 GLU Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 91 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.7980 chunk 227 optimal weight: 10.0000 chunk 139 optimal weight: 20.0000 chunk 108 optimal weight: 0.8980 chunk 158 optimal weight: 6.9990 chunk 239 optimal weight: 6.9990 chunk 220 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN D 258 GLN F 79 GLN F 93 ASN ** J 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 363 HIS ** K 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.5798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20637 Z= 0.219 Angle : 0.654 10.157 27996 Z= 0.338 Chirality : 0.046 0.181 3261 Planarity : 0.005 0.066 3519 Dihedral : 5.396 37.152 3678 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.21 % Allowed : 18.02 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.43 (0.17), residues: 2427 helix: 1.22 (0.26), residues: 441 sheet: 0.44 (0.22), residues: 582 loop : -1.13 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP O 36 HIS 0.008 0.001 HIS J 66 PHE 0.016 0.002 PHE J 53 TYR 0.037 0.002 TYR L 49 ARG 0.008 0.000 ARG F 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 330 time to evaluate : 2.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7876 (tm-30) cc_final: 0.6584 (tt0) REVERT: L 37 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7205 (tm-30) REVERT: C 80 ASP cc_start: 0.5000 (m-30) cc_final: 0.4750 (t0) REVERT: C 94 GLN cc_start: 0.7302 (tp-100) cc_final: 0.6942 (tp-100) REVERT: H 12 LYS cc_start: 0.5196 (OUTLIER) cc_final: 0.4914 (ttmt) REVERT: H 39 GLN cc_start: 0.7337 (OUTLIER) cc_final: 0.6787 (tp-100) REVERT: H 91 PHE cc_start: 0.6787 (OUTLIER) cc_final: 0.5846 (p90) REVERT: D 328 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7803 (tp-100) REVERT: D 372 VAL cc_start: 0.8318 (t) cc_final: 0.8034 (p) REVERT: D 446 SER cc_start: 0.8763 (m) cc_final: 0.8207 (p) REVERT: E 565 MET cc_start: 0.7312 (ptm) cc_final: 0.7030 (ttp) REVERT: E 567 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7593 (tp40) REVERT: I 19 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7929 (tmtt) REVERT: I 91 PHE cc_start: 0.6658 (OUTLIER) cc_final: 0.5560 (p90) REVERT: J 80 ASN cc_start: 0.6567 (p0) cc_final: 0.6351 (p0) REVERT: J 270 ILE cc_start: 0.8262 (mp) cc_final: 0.8048 (mt) REVERT: K 565 MET cc_start: 0.6948 (ptm) cc_final: 0.6349 (ttm) REVERT: K 629 MET cc_start: 0.7845 (mmm) cc_final: 0.7563 (mmm) REVERT: K 657 GLU cc_start: 0.7692 (tt0) cc_final: 0.7416 (tt0) REVERT: M 1 GLU cc_start: 0.6649 (mm-30) cc_final: 0.6430 (tm-30) REVERT: M 36 TYR cc_start: 0.6901 (m-80) cc_final: 0.6293 (m-80) REVERT: O 10 GLU cc_start: 0.5899 (OUTLIER) cc_final: 0.5657 (tm-30) REVERT: O 12 LYS cc_start: 0.6397 (tptt) cc_final: 0.5856 (tmtt) outliers start: 69 outliers final: 55 residues processed: 370 average time/residue: 0.2827 time to fit residues: 166.8661 Evaluate side-chains 378 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 314 time to evaluate : 2.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 216 HIS Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 328 GLN Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 496 ILE Chi-restraints excluded: chain E residue 564 HIS Chi-restraints excluded: chain E residue 567 GLN Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 216 HIS Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain J residue 439 ILE Chi-restraints excluded: chain J residue 496 ILE Chi-restraints excluded: chain K residue 540 GLN Chi-restraints excluded: chain K residue 564 HIS Chi-restraints excluded: chain K residue 592 LEU Chi-restraints excluded: chain K residue 618 THR Chi-restraints excluded: chain K residue 645 LEU Chi-restraints excluded: chain K residue 646 LEU Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain O residue 10 GLU Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 91 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.9980 chunk 202 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 175 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 190 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 195 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN J 363 HIS ** K 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.163268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.137309 restraints weight = 33869.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.140132 restraints weight = 17711.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.141244 restraints weight = 10915.667| |-----------------------------------------------------------------------------| r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.5882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 20637 Z= 0.206 Angle : 0.645 9.839 27996 Z= 0.332 Chirality : 0.046 0.170 3261 Planarity : 0.005 0.078 3519 Dihedral : 5.175 36.055 3678 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.03 % Allowed : 18.44 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.38 (0.17), residues: 2427 helix: 1.29 (0.26), residues: 441 sheet: 0.42 (0.22), residues: 600 loop : -1.10 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP O 36 HIS 0.005 0.001 HIS J 66 PHE 0.021 0.001 PHE J 53 TYR 0.036 0.002 TYR L 49 ARG 0.010 0.000 ARG N 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4225.52 seconds wall clock time: 76 minutes 35.59 seconds (4595.59 seconds total)