Starting phenix.real_space_refine on Thu Sep 26 12:01:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1b_11982/09_2024/7b1b_11982.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1b_11982/09_2024/7b1b_11982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1b_11982/09_2024/7b1b_11982.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1b_11982/09_2024/7b1b_11982.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1b_11982/09_2024/7b1b_11982.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1b_11982/09_2024/7b1b_11982.cif" } resolution = 4.23 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= 0.001 sd= 0.011 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 69 5.16 5 C 8162 2.51 5 N 2141 2.21 5 O 2498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12870 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 5484 Classifications: {'peptide': 754} Incomplete info: {'truncation_to_alanine': 154} Link IDs: {'PTRANS': 33, 'TRANS': 720} Unresolved non-hydrogen bonds: 564 Unresolved non-hydrogen angles: 691 Unresolved non-hydrogen dihedrals: 457 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 15, 'ASP:plan': 21, 'ASN:plan1': 13, 'HIS:plan': 6, 'PHE:plan': 4, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 369 Chain: "D" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 747 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 93} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "P" Number of atoms: 680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 680 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 86} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 5666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5666 Classifications: {'peptide': 752} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 33, 'TRANS': 718} Unresolved non-hydrogen bonds: 356 Unresolved non-hydrogen angles: 440 Unresolved non-hydrogen dihedrals: 280 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 16, 'ASN:plan1': 12, 'HIS:plan': 4, 'GLU:plan': 10, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 256 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" 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: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" 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: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 8.51, per 1000 atoms: 0.66 Number of scatterers: 12870 At special positions: 0 Unit cell: (101.26, 133.63, 164.34, 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 69 16.00 O 2498 8.00 N 2141 7.00 C 8162 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 46 " distance=2.02 Simple disulfide: pdb=" SG CYS A 44 " - pdb=" SG CYS A 57 " distance=2.04 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 104 " distance=2.03 Simple disulfide: pdb=" SG CYS A 559 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 561 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 616 " - pdb=" SG CYS A 622 " distance=2.03 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 767 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 783 " distance=2.03 Simple disulfide: pdb=" SG CYS D 10 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 47 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 56 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 59 " - pdb=" SG CYS P 59 " distance=2.03 Simple disulfide: pdb=" SG CYS D 94 " - pdb=" SG CYS P 94 " distance=2.03 Simple disulfide: pdb=" SG CYS P 10 " - pdb=" SG CYS P 65 " distance=2.03 Simple disulfide: pdb=" SG CYS P 47 " - pdb=" SG CYS P 95 " distance=2.02 Simple disulfide: pdb=" SG CYS P 56 " - pdb=" SG CYS P 97 " distance=2.02 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 46 " distance=2.03 Simple disulfide: pdb=" SG CYS B 44 " - pdb=" SG CYS B 57 " distance=2.03 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 104 " distance=2.04 Simple disulfide: pdb=" SG CYS B 559 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 561 " - pdb=" SG CYS B 608 " distance=2.03 Simple disulfide: pdb=" SG CYS B 616 " - pdb=" SG CYS B 622 " distance=2.03 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 767 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 783 " distance=2.03 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " NAG-ASN " NAG A 801 " - " ASN A 481 " " NAG A 802 " - " ASN A 521 " " NAG A 803 " - " ASN A 687 " " NAG C 1 " - " ASN A 634 " " NAG E 1 " - " ASN A 151 " " NAG G 1 " - " ASN A 194 " " NAG H 1 " - " ASN B 194 " " NAG I 1 " - " ASN B 151 " " NAG J 1 " - " ASN B 481 " " NAG K 1 " - " ASN B 521 " Time building additional restraints: 3.63 Conformation dependent library (CDL) restraints added in 1.7 seconds 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3288 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 21 sheets defined 11.3% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 111 through 116 Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.593A pdb=" N TYR A 142 " --> pdb=" O ASN A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 168 removed outlier: 3.528A pdb=" N SER A 167 " --> pdb=" O ARG A 163 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 163 through 168' Processing helix chain 'A' and resid 188 through 192 removed outlier: 3.817A pdb=" N ALA A 191 " --> pdb=" O THR A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 378 through 384 removed outlier: 3.763A pdb=" N LEU A 382 " --> pdb=" O PRO A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 454 removed outlier: 3.591A pdb=" N PHE A 453 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 495 Processing helix chain 'A' and resid 563 through 571 Processing helix chain 'A' and resid 602 through 606 Processing helix chain 'A' and resid 672 through 676 removed outlier: 3.714A pdb=" N LYS A 676 " --> pdb=" O ASN A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 723 removed outlier: 4.195A pdb=" N ALA A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 755 Processing helix chain 'A' and resid 756 through 759 Processing helix chain 'A' and resid 761 through 765 Processing helix chain 'D' and resid 25 through 29 removed outlier: 4.070A pdb=" N MET D 29 " --> pdb=" O ASN D 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 32 Processing helix chain 'B' and resid 84 through 88 Processing helix chain 'B' and resid 111 through 116 removed outlier: 3.524A pdb=" N SER B 115 " --> pdb=" O PRO B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 263 removed outlier: 4.141A pdb=" N PHE B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER B 263 " --> pdb=" O ASN B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 402 through 407 removed outlier: 3.508A pdb=" N ALA B 405 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B 407 " --> pdb=" O LYS B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 470 removed outlier: 3.593A pdb=" N VAL B 470 " --> pdb=" O PRO B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 493 removed outlier: 3.706A pdb=" N TRP B 491 " --> pdb=" O PHE B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 516 No H-bonds generated for 'chain 'B' and resid 514 through 516' Processing helix chain 'B' and resid 563 through 571 Processing helix chain 'B' and resid 602 through 606 Processing helix chain 'B' and resid 716 through 723 removed outlier: 3.978A pdb=" N LEU B 720 " --> pdb=" O ASP B 716 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA B 721 " --> pdb=" O ASP B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 4.263A pdb=" N ILE B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN B 755 " --> pdb=" O PHE B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 777 Processing helix chain 'B' and resid 778 through 783 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 48 removed outlier: 3.627A pdb=" N TYR A 56 " --> pdb=" O SER A 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 68 removed outlier: 6.338A pdb=" N VAL A 74 " --> pdb=" O THR A 100 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL A 102 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N PHE A 76 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 201 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN A 247 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR A 297 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN A 320 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 removed outlier: 7.337A pdb=" N ILE A 136 " --> pdb=" O VAL A 159 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 367 through 368 removed outlier: 6.723A pdb=" N LEU A 367 " --> pdb=" O TYR A 392 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU A 391 " --> pdb=" O HIS A 416 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU A 415 " --> pdb=" O TYR A 440 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE A 439 " --> pdb=" O HIS A 478 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU A 477 " --> pdb=" O ASP A 502 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 526 through 527 removed outlier: 6.216A pdb=" N LEU A 526 " --> pdb=" O ASN A 553 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 548 through 549 removed outlier: 6.741A pdb=" N ILE A 548 " --> pdb=" O GLN A 579 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 620 through 625 removed outlier: 3.573A pdb=" N GLU A 660 " --> pdb=" O VAL A 631 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 682 through 683 Processing sheet with id=AA9, first strand: chain 'D' and resid 13 through 17 Processing sheet with id=AB1, first strand: chain 'D' and resid 65 through 68 Processing sheet with id=AB2, first strand: chain 'D' and resid 87 through 89 removed outlier: 6.621A pdb=" N GLU D 87 " --> pdb=" O LEU D 74 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 12 through 15 Processing sheet with id=AB4, first strand: chain 'P' and resid 66 through 70 removed outlier: 5.796A pdb=" N LYS P 66 " --> pdb=" O CYS P 95 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N CYS P 95 " --> pdb=" O LYS P 66 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU P 68 " --> pdb=" O SER P 93 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 52 through 53 Processing sheet with id=AB6, first strand: chain 'B' and resid 64 through 66 Processing sheet with id=AB7, first strand: chain 'B' and resid 151 through 154 removed outlier: 6.389A pdb=" N LEU B 175 " --> pdb=" O GLY B 199 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 245 through 248 removed outlier: 6.423A pdb=" N VAL B 319 " --> pdb=" O ASN B 344 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B 367 " --> pdb=" O THR B 390 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR B 392 " --> pdb=" O LEU B 367 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 438 through 439 removed outlier: 3.730A pdb=" N HIS B 478 " --> pdb=" O ILE B 439 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP B 502 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 510 through 512 removed outlier: 6.880A pdb=" N LEU B 511 " --> pdb=" O LEU B 535 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 631 through 634 Processing sheet with id=AC3, first strand: chain 'B' and resid 682 through 683 160 hydrogen bonds defined for protein. 375 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.99 Time building geometry restraints manager: 4.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4256 1.34 - 1.47: 2868 1.47 - 1.59: 5889 1.59 - 1.71: 0 1.71 - 1.83: 86 Bond restraints: 13099 Sorted by residual: bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" C SER B 332 " pdb=" N LEU B 333 " ideal model delta sigma weight residual 1.332 1.307 0.025 1.40e-02 5.10e+03 3.20e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.02e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.92e+00 bond pdb=" CA TYR A 79 " pdb=" C TYR A 79 " ideal model delta sigma weight residual 1.522 1.492 0.029 1.72e-02 3.38e+03 2.89e+00 ... (remaining 13094 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.93: 17791 3.93 - 7.86: 91 7.86 - 11.79: 4 11.79 - 15.72: 0 15.72 - 19.65: 1 Bond angle restraints: 17887 Sorted by residual: angle pdb=" O LEU B 446 " pdb=" C LEU B 446 " pdb=" N ALA B 447 " ideal model delta sigma weight residual 122.75 103.10 19.65 1.16e+00 7.43e-01 2.87e+02 angle pdb=" C GLN B 442 " pdb=" CA GLN B 442 " pdb=" CB GLN B 442 " ideal model delta sigma weight residual 115.89 108.61 7.28 1.32e+00 5.74e-01 3.04e+01 angle pdb=" N VAL B 74 " pdb=" CA VAL B 74 " pdb=" C VAL B 74 " ideal model delta sigma weight residual 112.43 108.16 4.27 9.20e-01 1.18e+00 2.15e+01 angle pdb=" N VAL P 75 " pdb=" CA VAL P 75 " pdb=" C VAL P 75 " ideal model delta sigma weight residual 113.20 109.05 4.15 9.60e-01 1.09e+00 1.87e+01 angle pdb=" N GLU A 308 " pdb=" CA GLU A 308 " pdb=" CB GLU A 308 " ideal model delta sigma weight residual 113.65 108.63 5.02 1.47e+00 4.63e-01 1.17e+01 ... (remaining 17882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.85: 7663 23.85 - 47.70: 527 47.70 - 71.54: 63 71.54 - 95.39: 28 95.39 - 119.24: 23 Dihedral angle restraints: 8304 sinusoidal: 3283 harmonic: 5021 Sorted by residual: dihedral pdb=" CB CYS B 35 " pdb=" SG CYS B 35 " pdb=" SG CYS B 46 " pdb=" CB CYS B 46 " ideal model delta sinusoidal sigma weight residual 93.00 13.14 79.86 1 1.00e+01 1.00e-02 7.91e+01 dihedral pdb=" CB CYS B 616 " pdb=" SG CYS B 616 " pdb=" SG CYS B 622 " pdb=" CB CYS B 622 " ideal model delta sinusoidal sigma weight residual -86.00 -14.35 -71.65 1 1.00e+01 1.00e-02 6.58e+01 dihedral pdb=" CB CYS B 561 " pdb=" SG CYS B 561 " pdb=" SG CYS B 608 " pdb=" CB CYS B 608 " ideal model delta sinusoidal sigma weight residual 93.00 146.73 -53.73 1 1.00e+01 1.00e-02 3.92e+01 ... (remaining 8301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1895 0.062 - 0.124: 304 0.124 - 0.186: 20 0.186 - 0.248: 1 0.248 - 0.310: 6 Chirality restraints: 2226 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN B 151 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 2223 not shown) Planarity restraints: 2313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 446 " 0.086 2.00e-02 2.50e+03 1.54e-01 2.37e+02 pdb=" C LEU B 446 " -0.266 2.00e-02 2.50e+03 pdb=" O LEU B 446 " 0.097 2.00e-02 2.50e+03 pdb=" N ALA B 447 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 624 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.21e+00 pdb=" C MET B 624 " -0.031 2.00e-02 2.50e+03 pdb=" O MET B 624 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG B 625 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 76 " 0.016 2.00e-02 2.50e+03 1.29e-02 2.90e+00 pdb=" CG PHE B 76 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE B 76 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 76 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 76 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 76 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 76 " 0.005 2.00e-02 2.50e+03 ... (remaining 2310 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 451 2.65 - 3.21: 14565 3.21 - 3.77: 22646 3.77 - 4.34: 30374 4.34 - 4.90: 45189 Nonbonded interactions: 113225 Sorted by model distance: nonbonded pdb=" OG SER B 708 " pdb=" O ARG B 733 " model vdw 2.087 3.040 nonbonded pdb=" OG1 THR B 466 " pdb=" OD2 ASP B 490 " model vdw 2.118 3.040 nonbonded pdb=" O GLU A 418 " pdb=" ND2 ASN A 420 " model vdw 2.143 3.120 nonbonded pdb=" O HIS D 70 " pdb=" NH1 ARG D 72 " model vdw 2.145 3.120 nonbonded pdb=" OG SER A 504 " pdb=" ND2 ASN A 525 " model vdw 2.158 3.120 ... (remaining 113220 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 37 or (resid 38 through 43 and (name N or name \ CA or name C or name O or name CB )) or resid 44 through 46 or (resid 47 through \ 48 and (name N or name CA or name C or name O or name CB )) or resid 49 through \ 50 or (resid 51 through 53 and (name N or name CA or name C or name O or name C \ B )) or resid 54 through 58 or (resid 59 and (name N or name CA or name C or nam \ e O or name CB )) or resid 60 or (resid 61 and (name N or name CA or name C or n \ ame O or name CB )) or resid 62 through 66 or (resid 67 and (name N or name CA o \ r name C or name O or name CB )) or resid 68 or (resid 69 through 72 and (name N \ or name CA or name C or name O or name CB )) or resid 73 through 79 or (resid 8 \ 0 through 81 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 2 through 157 or (resid 158 and (name N or name CA or name C or name O or name C \ B )) or resid 159 through 406 or (resid 407 and (name N or name CA or name C or \ name O or name CB )) or resid 408 through 450 or (resid 451 and (name N or name \ CA or name C or name O or name CB )) or resid 452 through 454 or (resid 455 and \ (name N or name CA or name C or name O or name CB )) or resid 456 or (resid 457 \ and (name N or name CA or name C or name O or name CB )) or resid 458 or (resid \ 459 and (name N or name CA or name C or name O or name CB )) or resid 460 throug \ h 461 or (resid 462 through 465 and (name N or name CA or name C or name O or na \ me CB )) or resid 466 through 469 or (resid 470 through 473 and (name N or name \ CA or name C or name O or name CB )) or resid 474 through 644 or (resid 645 thro \ ugh 646 and (name N or name CA or name C or name O or name CB )) or resid 647 th \ rough 664 or (resid 665 and (name N or name CA or name C or name O or name CB )) \ or resid 666 through 675 or (resid 676 and (name N or name CA or name C or name \ O or name CB )) or resid 677 through 708 or (resid 709 and (name N or name CA o \ r name C or name O or name CB )) or resid 710 through 783)) selection = (chain 'B' and (resid 32 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 62 or (resid 63 and (name N or nam \ e CA or name C or name O or name CB )) or resid 64 through 74 or (resid 75 and ( \ name N or name CA or name C or name O or name CB )) or resid 76 through 83 or (r \ esid 84 through 88 and (name N or name CA or name C or name O or name CB )) or r \ esid 89 or (resid 90 and (name N or name CA or name C or name O or name CB )) or \ resid 91 through 92 or (resid 93 and (name N or name CA or name C or name O or \ name CB )) or resid 94 or (resid 95 through 96 and (name N or name CA or name C \ or name O or name CB )) or resid 97 through 102 or (resid 103 and (name N or nam \ e CA or name C or name O or name CB )) or resid 104 through 116 or (resid 117 an \ d (name N or name CA or name C or name O or name CB )) or resid 118 through 122 \ or (resid 123 and (name N or name CA or name C or name O or name CB )) or resid \ 124 through 132 or (resid 133 and (name N or name CA or name C or name O or name \ CB )) or resid 134 through 136 or (resid 137 and (name N or name CA or name C o \ r name O or name CB )) or resid 138 through 145 or (resid 146 and (name N or nam \ e CA or name C or name O or name CB )) or resid 147 or (resid 148 and (name N or \ name CA or name C or name O or name CB )) or resid 149 through 160 or (resid 16 \ 1 through 166 and (name N or name CA or name C or name O or name CB )) or resid \ 167 through 172 or (resid 173 and (name N or name CA or name C or name O or name \ CB )) or resid 174 through 177 or (resid 178 and (name N or name CA or name C o \ r name O or name CB )) or resid 179 through 180 or (resid 181 and (name N or nam \ e CA or name C or name O or name CB )) or resid 182 through 184 or (resid 185 an \ d (name N or name CA or name C or name O or name CB )) or resid 186 through 205 \ or (resid 206 through 209 and (name N or name CA or name C or name O or name CB \ )) or resid 210 through 211 or (resid 212 through 213 and (name N or name CA or \ name C or name O or name CB )) or resid 214 through 216 or (resid 217 through 21 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 219 or (resi \ d 220 through 221 and (name N or name CA or name C or name O or name CB )) or re \ sid 222 through 227 or (resid 228 and (name N or name CA or name C or name O or \ name CB )) or resid 229 or (resid 230 and (name N or name CA or name C or name O \ or name CB )) or resid 231 through 232 or (resid 233 through 234 and (name N or \ name CA or name C or name O or name CB )) or resid 235 or (resid 236 and (name \ N or name CA or name C or name O or name CB )) or resid 237 through 240 or (resi \ d 241 through 245 and (name N or name CA or name C or name O or name CB )) or re \ sid 246 through 248 or (resid 249 and (name N or name CA or name C or name O or \ name CB )) or resid 250 through 251 or (resid 252 and (name N or name CA or name \ C or name O or name CB )) or resid 253 or (resid 254 through 255 and (name N or \ name CA or name C or name O or name CB )) or resid 256 or (resid 257 through 25 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 260 through \ 264 or (resid 265 through 266 and (name N or name CA or name C or name O or name \ CB )) or resid 267 through 268 or (resid 269 and (name N or name CA or name C o \ r name O or name CB )) or resid 270 through 278 or (resid 279 and (name N or nam \ e CA or name C or name O or name CB )) or resid 280 through 281 or (resid 282 an \ d (name N or name CA or name C or name O or name CB )) or resid 283 through 285 \ or (resid 286 through 290 and (name N or name CA or name C or name O or name CB \ )) or resid 291 through 306 or (resid 307 and (name N or name CA or name C or na \ me O or name CB )) or resid 308 through 420 or (resid 421 and (name N or name CA \ or name C or name O or name CB )) or resid 422 through 443 or (resid 444 and (n \ ame N or name CA or name C or name O or name CB )) or resid 445 through 453 or ( \ resid 454 through 455 and (name N or name CA or name C or name O or name CB )) o \ r resid 456 through 559 or (resid 560 and (name N or name CA or name C or name O \ or name CB )) or resid 561 through 608 or (resid 609 and (name N or name CA or \ name C or name O or name CB )) or resid 610 or (resid 611 through 615 and (name \ N or name CA or name C or name O or name CB )) or resid 616 through 641 or (resi \ d 642 and (name N or name CA or name C or name O or name CB )) or resid 643 thro \ ugh 651 or (resid 652 through 655 and (name N or name CA or name C or name O or \ name CB )) or resid 656 or (resid 657 through 658 and (name N or name CA or name \ C or name O or name CB )) or resid 659 through 669 or (resid 670 and (name N or \ name CA or name C or name O or name CB )) or resid 671 through 693 or (resid 69 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 695 or (resi \ d 696 and (name N or name CA or name C or name O or name CB )) or resid 697 thro \ ugh 712 or (resid 713 and (name N or name CA or name C or name O or name CB )) o \ r resid 714 through 722 or (resid 723 through 725 and (name N or name CA or name \ C or name O or name CB )) or resid 726 through 764 or (resid 765 through 766 an \ d (name N or name CA or name C or name O or name CB )) or resid 767 through 769 \ or (resid 770 and (name N or name CA or name C or name O or name CB )) or (resid \ 771 through 773 and (name N or name CA or name C or name O or name CB )) or res \ id 774 or (resid 775 and (name N or name CA or name C or name O or name CB )) or \ resid 776 through 783)) } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = (chain 'D' and (resid 6 through 19 or (resid 20 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 34 or (resid 35 through \ 36 and (name N or name CA or name C or name O or name CB )) or resid 37 through \ 49 or (resid 50 through 52 and (name N or name CA or name C or name O or name CB \ )) or resid 53 or (resid 54 and (name N or name CA or name C or name O or name \ CB )) or resid 55 through 59 or (resid 60 through 61 and (name N or name CA or n \ ame C or name O or name CB )) or resid 62 or (resid 63 and (name N or name CA or \ name C or name O or name CB )) or resid 64 through 82 or (resid 83 and (name N \ or name CA or name C or name O or name CB )) or resid 84 through 85 or (resid 86 \ through 88 and (name N or name CA or name C or name O or name CB )) or resid 89 \ through 97)) selection = (chain 'P' and (resid 6 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 23 or (resid 24 through 28 and (nam \ e N or name CA or name C or name O or name CB )) or resid 29 through 38 or (resi \ d 39 through 40 and (name N or name CA or name C or name O or name CB )) or resi \ d 41 through 79 or (resid 80 and (name N or name CA or name C or name O or name \ CB )) or resid 81 through 97)) } ncs_group { reference = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 3.180 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: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 31.790 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 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 : 0.004 0.063 13099 Z= 0.289 Angle : 0.752 19.649 17887 Z= 0.384 Chirality : 0.046 0.310 2226 Planarity : 0.005 0.154 2303 Dihedral : 17.240 119.239 4938 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 33.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.62 % Favored : 86.38 % Rotamer: Outliers : 0.54 % Allowed : 27.91 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.20), residues: 1689 helix: -1.34 (0.58), residues: 87 sheet: -1.87 (0.33), residues: 254 loop : -2.11 (0.16), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 31 HIS 0.007 0.001 HIS A 132 PHE 0.029 0.001 PHE B 76 TYR 0.014 0.002 TYR B 129 ARG 0.003 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 22 time to evaluate : 1.473 Fit side-chains revert: symmetry clash REVERT: A 441 MET cc_start: 0.8773 (tpp) cc_final: 0.8460 (tpp) REVERT: B 498 MET cc_start: 0.9197 (tpp) cc_final: 0.8729 (tpp) outliers start: 7 outliers final: 1 residues processed: 28 average time/residue: 0.1910 time to fit residues: 10.4226 Evaluate side-chains 23 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 70 optimal weight: 20.0000 chunk 43 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN ** A 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 GLN ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13099 Z= 0.270 Angle : 0.742 11.259 17887 Z= 0.367 Chirality : 0.047 0.236 2226 Planarity : 0.005 0.093 2303 Dihedral : 12.462 113.161 2224 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 23.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.66 % Favored : 88.34 % Rotamer: Outliers : 0.08 % Allowed : 5.67 % Favored : 94.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.20), residues: 1689 helix: -1.67 (0.51), residues: 100 sheet: -1.67 (0.33), residues: 263 loop : -2.12 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 31 HIS 0.007 0.001 HIS A 478 PHE 0.023 0.002 PHE B 166 TYR 0.020 0.002 TYR A 684 ARG 0.006 0.001 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 1.530 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 23 average time/residue: 0.2042 time to fit residues: 9.4606 Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 126 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 152 optimal weight: 20.0000 chunk 165 optimal weight: 20.0000 chunk 136 optimal weight: 9.9990 chunk 151 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 ASN B 411 ASN ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13099 Z= 0.233 Angle : 0.678 9.789 17887 Z= 0.334 Chirality : 0.046 0.237 2226 Planarity : 0.004 0.085 2303 Dihedral : 9.638 111.688 2224 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 21.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.89 % Favored : 89.11 % Rotamer: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.20), residues: 1689 helix: -1.86 (0.48), residues: 100 sheet: -1.78 (0.32), residues: 265 loop : -2.12 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP P 31 HIS 0.009 0.002 HIS B 395 PHE 0.027 0.002 PHE B 381 TYR 0.021 0.002 TYR A 684 ARG 0.007 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.597 Fit side-chains revert: symmetry clash REVERT: A 441 MET cc_start: 0.8773 (mmp) cc_final: 0.8432 (tpp) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2100 time to fit residues: 9.4178 Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 9.9990 chunk 114 optimal weight: 20.0000 chunk 79 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 153 optimal weight: 20.0000 chunk 162 optimal weight: 30.0000 chunk 80 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN D 18 HIS D 88 GLN B 373 GLN ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 13099 Z= 0.395 Angle : 0.799 11.392 17887 Z= 0.392 Chirality : 0.046 0.240 2226 Planarity : 0.005 0.077 2303 Dihedral : 8.839 113.622 2224 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 28.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.03 % Favored : 86.92 % Rotamer: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.20), residues: 1689 helix: -1.76 (0.48), residues: 105 sheet: -2.03 (0.31), residues: 273 loop : -2.19 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP P 31 HIS 0.008 0.002 HIS A 677 PHE 0.021 0.002 PHE D 69 TYR 0.018 0.002 TYR B 684 ARG 0.009 0.001 ARG A 480 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 441 MET cc_start: 0.8831 (mmp) cc_final: 0.8606 (tpp) REVERT: B 498 MET cc_start: 0.9249 (tpt) cc_final: 0.8957 (tpp) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2223 time to fit residues: 9.4119 Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 120 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 82 optimal weight: 8.9990 chunk 145 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13099 Z= 0.309 Angle : 0.729 10.702 17887 Z= 0.360 Chirality : 0.046 0.239 2226 Planarity : 0.005 0.103 2303 Dihedral : 8.583 112.395 2224 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 24.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.14 % Favored : 87.80 % Rotamer: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.19), residues: 1689 helix: -1.59 (0.51), residues: 94 sheet: -1.75 (0.33), residues: 246 loop : -2.25 (0.16), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP P 31 HIS 0.008 0.002 HIS A 132 PHE 0.023 0.002 PHE A 610 TYR 0.018 0.002 TYR A 684 ARG 0.011 0.001 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 441 MET cc_start: 0.8835 (mmp) cc_final: 0.8598 (tpp) REVERT: B 498 MET cc_start: 0.9326 (tpt) cc_final: 0.9017 (tpp) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.2173 time to fit residues: 9.9973 Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 2.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 30.0000 chunk 146 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 134 optimal weight: 0.8980 chunk 75 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13099 Z= 0.251 Angle : 0.688 12.223 17887 Z= 0.338 Chirality : 0.045 0.242 2226 Planarity : 0.004 0.068 2303 Dihedral : 8.326 111.804 2224 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 22.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.72 % Favored : 88.22 % Rotamer: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.20), residues: 1689 helix: -1.61 (0.51), residues: 94 sheet: -1.75 (0.33), residues: 251 loop : -2.19 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP P 31 HIS 0.007 0.001 HIS A 132 PHE 0.020 0.002 PHE B 76 TYR 0.016 0.002 TYR A 684 ARG 0.008 0.001 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 441 MET cc_start: 0.8798 (mmp) cc_final: 0.8523 (tpp) REVERT: B 498 MET cc_start: 0.9358 (tpt) cc_final: 0.9008 (tpp) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.2047 time to fit residues: 9.5246 Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 118 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 74 optimal weight: 40.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 GLN ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 HIS ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13099 Z= 0.191 Angle : 0.653 11.732 17887 Z= 0.320 Chirality : 0.044 0.243 2226 Planarity : 0.004 0.081 2303 Dihedral : 8.037 110.583 2224 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.07 % Favored : 88.87 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.20), residues: 1689 helix: -1.29 (0.53), residues: 88 sheet: -1.61 (0.32), residues: 261 loop : -2.11 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 31 HIS 0.006 0.001 HIS A 132 PHE 0.019 0.001 PHE B 76 TYR 0.014 0.001 TYR A 684 ARG 0.008 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 498 MET cc_start: 0.9365 (tpt) cc_final: 0.9018 (tpp) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.2064 time to fit residues: 9.8188 Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 96 optimal weight: 20.0000 chunk 48 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 102 optimal weight: 8.9990 chunk 110 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 147 optimal weight: 20.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 ASN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13099 Z= 0.274 Angle : 0.694 11.544 17887 Z= 0.341 Chirality : 0.045 0.238 2226 Planarity : 0.004 0.071 2303 Dihedral : 8.123 110.893 2224 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 22.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.66 % Favored : 88.28 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.20), residues: 1689 helix: -1.27 (0.54), residues: 88 sheet: -1.84 (0.32), residues: 262 loop : -2.14 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP P 31 HIS 0.007 0.001 HIS A 132 PHE 0.017 0.002 PHE B 76 TYR 0.016 0.002 TYR B 197 ARG 0.010 0.001 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 498 MET cc_start: 0.9357 (tpt) cc_final: 0.9105 (tpp) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2292 time to fit residues: 9.7142 Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 10.0000 chunk 141 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 90 optimal weight: 0.0770 chunk 65 optimal weight: 10.0000 chunk 118 optimal weight: 0.0030 chunk 46 optimal weight: 20.0000 chunk 136 optimal weight: 0.7980 chunk 142 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 159 optimal weight: 0.8980 overall best weight: 0.7550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 HIS D 88 GLN ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13099 Z= 0.157 Angle : 0.655 11.403 17887 Z= 0.317 Chirality : 0.045 0.241 2226 Planarity : 0.004 0.040 2303 Dihedral : 7.721 108.505 2224 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.71 % Favored : 90.23 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.20), residues: 1689 helix: -1.39 (0.51), residues: 100 sheet: -1.68 (0.32), residues: 260 loop : -2.12 (0.16), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 31 HIS 0.005 0.001 HIS A 132 PHE 0.019 0.001 PHE B 76 TYR 0.015 0.001 TYR A 684 ARG 0.005 0.001 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 498 MET cc_start: 0.9383 (tpt) cc_final: 0.9026 (tpp) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2018 time to fit residues: 9.0123 Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 9.9990 chunk 75 optimal weight: 0.0030 chunk 110 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 154 optimal weight: 0.8980 chunk 133 optimal weight: 0.5980 chunk 13 optimal weight: 7.9990 chunk 102 optimal weight: 0.0770 chunk 81 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 overall best weight: 1.3150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13099 Z= 0.155 Angle : 0.626 11.080 17887 Z= 0.303 Chirality : 0.044 0.295 2226 Planarity : 0.004 0.041 2303 Dihedral : 7.499 106.156 2224 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.00 % Favored : 90.94 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.20), residues: 1689 helix: -1.34 (0.50), residues: 105 sheet: -1.63 (0.32), residues: 260 loop : -2.04 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 31 HIS 0.005 0.001 HIS A 132 PHE 0.016 0.001 PHE B 76 TYR 0.015 0.001 TYR A 440 ARG 0.004 0.000 ARG D 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.637 Fit side-chains revert: symmetry clash REVERT: A 441 MET cc_start: 0.8767 (mmp) cc_final: 0.8399 (tpp) REVERT: A 498 MET cc_start: 0.8226 (tpt) cc_final: 0.7652 (tpt) REVERT: B 498 MET cc_start: 0.9353 (tpt) cc_final: 0.9089 (tpp) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2052 time to fit residues: 9.1883 Evaluate side-chains 22 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 8.9990 chunk 122 optimal weight: 0.8980 chunk 19 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 137 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 overall best weight: 6.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 18 HIS ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.025110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.018519 restraints weight = 262113.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.018962 restraints weight = 185493.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.019264 restraints weight = 144037.955| |-----------------------------------------------------------------------------| r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 13099 Z= 0.351 Angle : 0.756 11.060 17887 Z= 0.370 Chirality : 0.045 0.335 2226 Planarity : 0.005 0.064 2303 Dihedral : 8.079 110.983 2224 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 23.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.43 % Favored : 88.51 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.20), residues: 1689 helix: -1.43 (0.51), residues: 100 sheet: -1.85 (0.32), residues: 269 loop : -2.10 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP P 31 HIS 0.008 0.002 HIS A 132 PHE 0.016 0.002 PHE D 69 TYR 0.019 0.002 TYR B 684 ARG 0.007 0.001 ARG D 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1979.19 seconds wall clock time: 36 minutes 55.00 seconds (2215.00 seconds total)