Starting phenix.real_space_refine on Sat Jan 20 01:55:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zep_14691/01_2024/7zep_14691.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zep_14691/01_2024/7zep_14691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zep_14691/01_2024/7zep_14691.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zep_14691/01_2024/7zep_14691.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zep_14691/01_2024/7zep_14691.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zep_14691/01_2024/7zep_14691.pdb" } resolution = 3.2 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= 0.099 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 86 5.16 5 C 8504 2.51 5 N 2320 2.21 5 O 2412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13324 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6661 Classifications: {'peptide': 827} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 784} Chain breaks: 3 Chain: "B" Number of atoms: 6661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6661 Classifications: {'peptide': 827} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 784} Chain breaks: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2029 SG CYS A 287 52.541 75.712 51.905 1.00 77.66 S ATOM 2306 SG CYS A 321 53.320 76.554 48.500 1.00 56.85 S ATOM 2312 SG CYS A 322 52.404 72.920 49.565 1.00 53.20 S ATOM 8690 SG CYS B 287 71.196 26.443 51.859 1.00 80.24 S ATOM 8967 SG CYS B 321 70.245 25.851 48.220 1.00 56.62 S ATOM 8973 SG CYS B 322 71.189 29.368 49.398 1.00 53.63 S Time building chain proxies: 6.92, per 1000 atoms: 0.52 Number of scatterers: 13324 At special positions: 0 Unit cell: (124.474, 103.554, 126.566, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 86 16.00 O 2412 8.00 N 2320 7.00 C 8504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.37 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 321 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 285 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 287 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 322 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" ND1 HIS B 285 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 321 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 322 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 287 " Number of angles added : 6 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3124 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 16 sheets defined 45.0% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 27 through 33 removed outlier: 3.769A pdb=" N LYS A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 56 Processing helix chain 'A' and resid 74 through 86 Processing helix chain 'A' and resid 144 through 157 removed outlier: 3.608A pdb=" N LYS A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 4.072A pdb=" N ILE A 193 " --> pdb=" O PRO A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 241 Proline residue: A 232 - end of helix Proline residue: A 236 - end of helix removed outlier: 3.626A pdb=" N THR A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 280 removed outlier: 3.528A pdb=" N LYS A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 353 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.567A pdb=" N GLU A 388 " --> pdb=" O LYS A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 398 Processing helix chain 'A' and resid 409 through 420 Processing helix chain 'A' and resid 422 through 431 removed outlier: 3.513A pdb=" N GLN A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 449 Processing helix chain 'A' and resid 482 through 501 Processing helix chain 'A' and resid 536 through 540 Processing helix chain 'A' and resid 543 through 560 removed outlier: 3.667A pdb=" N ILE A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 560 " --> pdb=" O ILE A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 586 removed outlier: 3.638A pdb=" N ILE A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 589 No H-bonds generated for 'chain 'A' and resid 587 through 589' Processing helix chain 'A' and resid 604 through 621 removed outlier: 3.658A pdb=" N MET A 613 " --> pdb=" O ALA A 609 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU A 614 " --> pdb=" O MET A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 625 No H-bonds generated for 'chain 'A' and resid 623 through 625' Processing helix chain 'A' and resid 633 through 643 removed outlier: 3.533A pdb=" N ARG A 637 " --> pdb=" O ASN A 633 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG A 643 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 657 Processing helix chain 'A' and resid 669 through 673 Processing helix chain 'A' and resid 679 through 690 removed outlier: 3.506A pdb=" N LYS A 683 " --> pdb=" O ASP A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 707 removed outlier: 3.839A pdb=" N THR A 707 " --> pdb=" O TYR A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 721 Processing helix chain 'A' and resid 734 through 751 removed outlier: 3.752A pdb=" N VAL A 747 " --> pdb=" O LYS A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 763 removed outlier: 3.642A pdb=" N GLU A 762 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 763 " --> pdb=" O CYS A 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 759 through 763' Processing helix chain 'A' and resid 784 through 803 removed outlier: 3.526A pdb=" N CYS A 791 " --> pdb=" O GLN A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 807 No H-bonds generated for 'chain 'A' and resid 805 through 807' Processing helix chain 'A' and resid 815 through 817 No H-bonds generated for 'chain 'A' and resid 815 through 817' Processing helix chain 'A' and resid 818 through 831 removed outlier: 3.506A pdb=" N TYR A 824 " --> pdb=" O GLU A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 834 No H-bonds generated for 'chain 'A' and resid 832 through 834' Processing helix chain 'A' and resid 855 through 858 Processing helix chain 'A' and resid 877 through 887 removed outlier: 4.004A pdb=" N LEU A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE A 883 " --> pdb=" O PRO A 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 34 removed outlier: 4.097A pdb=" N LYS B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU B 34 " --> pdb=" O ASN B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 56 Processing helix chain 'B' and resid 74 through 86 Processing helix chain 'B' and resid 144 through 157 removed outlier: 3.595A pdb=" N LYS B 157 " --> pdb=" O LYS B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 removed outlier: 3.978A pdb=" N ILE B 193 " --> pdb=" O PRO B 189 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 240 removed outlier: 3.520A pdb=" N VAL B 227 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS B 228 " --> pdb=" O GLN B 224 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) Proline residue: B 232 - end of helix Proline residue: B 236 - end of helix Processing helix chain 'B' and resid 266 through 280 removed outlier: 3.885A pdb=" N ARG B 272 " --> pdb=" O ASP B 268 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS B 273 " --> pdb=" O SER B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 353 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.674A pdb=" N LEU B 387 " --> pdb=" O SER B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 398 removed outlier: 3.528A pdb=" N GLN B 395 " --> pdb=" O LYS B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 420 Processing helix chain 'B' and resid 422 through 431 Processing helix chain 'B' and resid 444 through 449 Processing helix chain 'B' and resid 482 through 501 Processing helix chain 'B' and resid 536 through 540 Processing helix chain 'B' and resid 543 through 560 removed outlier: 3.539A pdb=" N SER B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE B 556 " --> pdb=" O GLN B 552 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY B 560 " --> pdb=" O ILE B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 586 removed outlier: 3.627A pdb=" N ILE B 584 " --> pdb=" O GLN B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 589 No H-bonds generated for 'chain 'B' and resid 587 through 589' Processing helix chain 'B' and resid 604 through 621 Processing helix chain 'B' and resid 623 through 625 No H-bonds generated for 'chain 'B' and resid 623 through 625' Processing helix chain 'B' and resid 633 through 643 removed outlier: 3.831A pdb=" N ARG B 643 " --> pdb=" O PHE B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 657 Processing helix chain 'B' and resid 669 through 673 Processing helix chain 'B' and resid 679 through 690 Processing helix chain 'B' and resid 703 through 707 removed outlier: 3.845A pdb=" N THR B 707 " --> pdb=" O TYR B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 721 Processing helix chain 'B' and resid 734 through 751 removed outlier: 3.818A pdb=" N VAL B 747 " --> pdb=" O LYS B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 763 removed outlier: 3.595A pdb=" N GLU B 762 " --> pdb=" O GLY B 759 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL B 763 " --> pdb=" O CYS B 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 759 through 763' Processing helix chain 'B' and resid 784 through 803 removed outlier: 3.513A pdb=" N MET B 789 " --> pdb=" O VAL B 785 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B 790 " --> pdb=" O GLU B 786 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 807 No H-bonds generated for 'chain 'B' and resid 805 through 807' Processing helix chain 'B' and resid 815 through 817 No H-bonds generated for 'chain 'B' and resid 815 through 817' Processing helix chain 'B' and resid 818 through 831 Processing helix chain 'B' and resid 832 through 834 No H-bonds generated for 'chain 'B' and resid 832 through 834' Processing helix chain 'B' and resid 855 through 858 removed outlier: 3.609A pdb=" N SER B 858 " --> pdb=" O ARG B 855 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 855 through 858' Processing helix chain 'B' and resid 877 through 887 removed outlier: 3.973A pdb=" N LEU B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE B 883 " --> pdb=" O PRO B 879 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 11 removed outlier: 4.688A pdb=" N VAL A 18 " --> pdb=" O GLU A 11 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE A 19 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ALA A 64 " --> pdb=" O ILE A 19 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N VAL A 21 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 136 Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 200 removed outlier: 6.717A pdb=" N LEU A 199 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR A 296 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE A 315 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS A 298 " --> pdb=" O CYS A 313 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N CYS A 313 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL A 300 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR A 311 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL A 302 " --> pdb=" O TYR A 309 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLU A 214 " --> pdb=" O PHE A 247 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 283 through 284 removed outlier: 3.590A pdb=" N ALA A 323 " --> pdb=" O VAL A 284 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 332 through 335 Processing sheet with id=AA6, first strand: chain 'A' and resid 405 through 408 removed outlier: 6.274A pdb=" N ARG A 406 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N PHE A 441 " --> pdb=" O ARG A 406 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR A 408 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N CYS A 459 " --> pdb=" O ILE A 475 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 647 through 650 removed outlier: 6.550A pdb=" N ILE A 627 " --> pdb=" O ARG A 647 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N GLU A 649 " --> pdb=" O ILE A 627 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N TYR A 629 " --> pdb=" O GLU A 649 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU A 628 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE A 665 " --> pdb=" O TRP A 699 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N PHE A 701 " --> pdb=" O ILE A 665 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE A 667 " --> pdb=" O PHE A 701 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU A 595 " --> pdb=" O ILE A 700 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LEU A 702 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N VAL A 597 " --> pdb=" O LEU A 702 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 776 through 779 removed outlier: 6.291A pdb=" N SER A 863 " --> pdb=" O HIS A 892 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N TYR A 894 " --> pdb=" O SER A 863 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL A 865 " --> pdb=" O TYR A 894 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N PHE A 896 " --> pdb=" O VAL A 865 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLY A 867 " --> pdb=" O PHE A 896 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 18 through 23 removed outlier: 6.260A pdb=" N ILE B 19 " --> pdb=" O ARG B 62 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ALA B 64 " --> pdb=" O ILE B 19 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N VAL B 21 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 133 through 136 Processing sheet with id=AB2, first strand: chain 'B' and resid 198 through 200 removed outlier: 6.572A pdb=" N THR B 296 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE B 315 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS B 298 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N CYS B 313 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL B 300 " --> pdb=" O TYR B 311 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR B 311 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL B 302 " --> pdb=" O TYR B 309 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU B 214 " --> pdb=" O PHE B 247 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 283 through 284 removed outlier: 3.633A pdb=" N ALA B 323 " --> pdb=" O VAL B 284 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 332 through 335 Processing sheet with id=AB5, first strand: chain 'B' and resid 405 through 408 removed outlier: 6.316A pdb=" N ARG B 406 " --> pdb=" O LEU B 439 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N PHE B 441 " --> pdb=" O ARG B 406 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR B 408 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS B 459 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 647 through 650 removed outlier: 6.100A pdb=" N LEU B 628 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE B 665 " --> pdb=" O TRP B 699 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N PHE B 701 " --> pdb=" O ILE B 665 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE B 667 " --> pdb=" O PHE B 701 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU B 595 " --> pdb=" O ILE B 700 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU B 702 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N VAL B 597 " --> pdb=" O LEU B 702 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 776 through 779 removed outlier: 7.233A pdb=" N SER B 863 " --> pdb=" O LYS B 890 " (cutoff:3.500A) 563 hydrogen bonds defined for protein. 1593 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: 4.70 Time building geometry restraints manager: 5.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4346 1.34 - 1.46: 2830 1.46 - 1.58: 6312 1.58 - 1.69: 0 1.69 - 1.81: 122 Bond restraints: 13610 Sorted by residual: bond pdb=" CG PRO B 409 " pdb=" CD PRO B 409 " ideal model delta sigma weight residual 1.512 1.488 0.024 2.70e-02 1.37e+03 8.07e-01 bond pdb=" CG PRO A 409 " pdb=" CD PRO A 409 " ideal model delta sigma weight residual 1.512 1.488 0.024 2.70e-02 1.37e+03 8.00e-01 bond pdb=" CA PRO B 12 " pdb=" C PRO B 12 " ideal model delta sigma weight residual 1.528 1.521 0.008 9.10e-03 1.21e+04 7.11e-01 bond pdb=" CA ILE B 231 " pdb=" C ILE B 231 " ideal model delta sigma weight residual 1.520 1.527 -0.007 8.80e-03 1.29e+04 6.75e-01 bond pdb=" CB PRO B 236 " pdb=" CG PRO B 236 " ideal model delta sigma weight residual 1.492 1.453 0.039 5.00e-02 4.00e+02 6.20e-01 ... (remaining 13605 not shown) Histogram of bond angle deviations from ideal: 99.52 - 106.43: 404 106.43 - 113.33: 7263 113.33 - 120.23: 4868 120.23 - 127.14: 5702 127.14 - 134.04: 137 Bond angle restraints: 18374 Sorted by residual: angle pdb=" C GLU B 137 " pdb=" CA GLU B 137 " pdb=" CB GLU B 137 " ideal model delta sigma weight residual 110.42 116.21 -5.79 1.99e+00 2.53e-01 8.47e+00 angle pdb=" C GLU A 137 " pdb=" CA GLU A 137 " pdb=" CB GLU A 137 " ideal model delta sigma weight residual 110.42 116.06 -5.64 1.99e+00 2.53e-01 8.04e+00 angle pdb=" C CYS A 287 " pdb=" N GLN A 288 " pdb=" CA GLN A 288 " ideal model delta sigma weight residual 122.28 126.10 -3.82 1.77e+00 3.19e-01 4.66e+00 angle pdb=" CA GLN A 288 " pdb=" CB GLN A 288 " pdb=" CG GLN A 288 " ideal model delta sigma weight residual 114.10 118.23 -4.13 2.00e+00 2.50e-01 4.26e+00 angle pdb=" CA GLN B 288 " pdb=" CB GLN B 288 " pdb=" CG GLN B 288 " ideal model delta sigma weight residual 114.10 118.14 -4.04 2.00e+00 2.50e-01 4.07e+00 ... (remaining 18369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 7506 17.84 - 35.69: 631 35.69 - 53.53: 136 53.53 - 71.38: 28 71.38 - 89.22: 15 Dihedral angle restraints: 8316 sinusoidal: 3484 harmonic: 4832 Sorted by residual: dihedral pdb=" CA ASP A 191 " pdb=" CB ASP A 191 " pdb=" CG ASP A 191 " pdb=" OD1 ASP A 191 " ideal model delta sinusoidal sigma weight residual -30.00 -87.21 57.21 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CG ARG B 406 " pdb=" CD ARG B 406 " pdb=" NE ARG B 406 " pdb=" CZ ARG B 406 " ideal model delta sinusoidal sigma weight residual 180.00 -135.08 -44.92 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CA ARG B 724 " pdb=" C ARG B 724 " pdb=" N GLU B 725 " pdb=" CA GLU B 725 " ideal model delta harmonic sigma weight residual 180.00 163.73 16.27 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 8313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1206 0.027 - 0.054: 522 0.054 - 0.082: 133 0.082 - 0.109: 109 0.109 - 0.136: 48 Chirality restraints: 2018 Sorted by residual: chirality pdb=" CA GLN A 288 " pdb=" N GLN A 288 " pdb=" C GLN A 288 " pdb=" CB GLN A 288 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA ILE B 464 " pdb=" N ILE B 464 " pdb=" C ILE B 464 " pdb=" CB ILE B 464 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA ILE A 464 " pdb=" N ILE A 464 " pdb=" C ILE A 464 " pdb=" CB ILE A 464 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 2015 not shown) Planarity restraints: 2360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 231 " -0.033 5.00e-02 4.00e+02 5.05e-02 4.08e+00 pdb=" N PRO B 232 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 232 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 232 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 288 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO B 289 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 289 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 289 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 235 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO B 236 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.023 5.00e-02 4.00e+02 ... (remaining 2357 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2031 2.76 - 3.30: 12251 3.30 - 3.83: 21091 3.83 - 4.37: 26288 4.37 - 4.90: 45867 Nonbonded interactions: 107528 Sorted by model distance: nonbonded pdb=" O GLU A 424 " pdb=" ND2 ASN A 428 " model vdw 2.231 2.520 nonbonded pdb=" OD2 ASP A 703 " pdb=" NE2 GLN A 706 " model vdw 2.258 2.520 nonbonded pdb=" OD1 ASP A 191 " pdb=" OH TYR A 245 " model vdw 2.262 2.440 nonbonded pdb=" O LEU A 558 " pdb=" OG SER A 566 " model vdw 2.270 2.440 nonbonded pdb=" N ALA B 841 " pdb=" OD2 ASP B 852 " model vdw 2.272 2.520 ... (remaining 107523 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 7.570 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 40.980 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 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 : 0.002 0.039 13610 Z= 0.136 Angle : 0.475 5.792 18374 Z= 0.259 Chirality : 0.040 0.136 2018 Planarity : 0.004 0.050 2360 Dihedral : 14.255 89.224 5192 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.20), residues: 1638 helix: 0.08 (0.20), residues: 642 sheet: 0.57 (0.31), residues: 268 loop : 0.25 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 413 HIS 0.002 0.000 HIS B 848 PHE 0.013 0.001 PHE B 218 TYR 0.013 0.001 TYR A 629 ARG 0.007 0.000 ARG B 643 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.743 Fit side-chains REVERT: A 196 LYS cc_start: 0.8503 (ttmm) cc_final: 0.8252 (ttmm) REVERT: A 316 ARG cc_start: 0.7610 (ttt90) cc_final: 0.7184 (tpt170) REVERT: A 621 HIS cc_start: 0.7936 (m-70) cc_final: 0.7514 (m170) REVERT: B 710 LEU cc_start: 0.8069 (mt) cc_final: 0.7842 (mt) REVERT: B 852 ASP cc_start: 0.7055 (m-30) cc_final: 0.6643 (m-30) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2951 time to fit residues: 75.1592 Evaluate side-chains 150 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 68 optimal weight: 0.0970 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 66 optimal weight: 0.0870 chunk 128 optimal weight: 0.0040 chunk 49 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 overall best weight: 0.3970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 592 ASN ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN ** B 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13610 Z= 0.157 Angle : 0.494 7.192 18374 Z= 0.258 Chirality : 0.042 0.141 2018 Planarity : 0.004 0.045 2360 Dihedral : 3.611 15.934 1824 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.47 % Allowed : 5.35 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.90 (0.20), residues: 1638 helix: 1.00 (0.20), residues: 656 sheet: 0.65 (0.31), residues: 270 loop : 0.38 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 413 HIS 0.003 0.000 HIS A 285 PHE 0.014 0.001 PHE A 218 TYR 0.012 0.001 TYR B 629 ARG 0.005 0.000 ARG B 643 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 166 time to evaluate : 1.526 Fit side-chains revert: symmetry clash REVERT: A 196 LYS cc_start: 0.8505 (ttmm) cc_final: 0.8016 (ttmt) REVERT: A 621 HIS cc_start: 0.7963 (m-70) cc_final: 0.7568 (m170) REVERT: B 583 GLU cc_start: 0.7334 (mm-30) cc_final: 0.7124 (mm-30) REVERT: B 610 MET cc_start: 0.7767 (mtp) cc_final: 0.7526 (mtm) REVERT: B 710 LEU cc_start: 0.8053 (mt) cc_final: 0.7836 (mt) outliers start: 7 outliers final: 5 residues processed: 169 average time/residue: 0.2757 time to fit residues: 67.0272 Evaluate side-chains 157 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 152 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 882 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 123 optimal weight: 0.0020 chunk 101 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 161 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 119 optimal weight: 0.0870 overall best weight: 0.5566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 618 ASN ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN B 217 GLN B 618 ASN ** B 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13610 Z= 0.174 Angle : 0.467 6.879 18374 Z= 0.240 Chirality : 0.041 0.138 2018 Planarity : 0.004 0.039 2360 Dihedral : 3.594 16.111 1824 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.81 % Allowed : 7.05 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.21), residues: 1638 helix: 1.44 (0.20), residues: 646 sheet: 0.58 (0.31), residues: 270 loop : 0.37 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 413 HIS 0.003 0.001 HIS B 869 PHE 0.015 0.001 PHE A 218 TYR 0.012 0.001 TYR B 629 ARG 0.008 0.000 ARG B 690 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 163 time to evaluate : 1.765 Fit side-chains REVERT: A 196 LYS cc_start: 0.8487 (ttmm) cc_final: 0.8168 (ttmm) REVERT: A 225 GLU cc_start: 0.6565 (tm-30) cc_final: 0.5645 (tm-30) REVERT: A 229 ARG cc_start: 0.7974 (ttp-170) cc_final: 0.7760 (mtm110) REVERT: A 311 TYR cc_start: 0.7074 (m-80) cc_final: 0.6807 (m-80) REVERT: A 621 HIS cc_start: 0.7901 (m-70) cc_final: 0.7548 (m170) REVERT: A 725 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7373 (tp30) REVERT: A 780 LYS cc_start: 0.7499 (mttt) cc_final: 0.7189 (mmtt) REVERT: B 710 LEU cc_start: 0.8024 (mt) cc_final: 0.7808 (mt) outliers start: 12 outliers final: 10 residues processed: 169 average time/residue: 0.2891 time to fit residues: 69.6926 Evaluate side-chains 168 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 157 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 882 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 0.1980 chunk 112 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 ASN ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 13610 Z= 0.469 Angle : 0.615 7.734 18374 Z= 0.313 Chirality : 0.048 0.139 2018 Planarity : 0.005 0.041 2360 Dihedral : 4.119 19.090 1824 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.56 % Allowed : 8.40 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.61 (0.20), residues: 1638 helix: 0.98 (0.20), residues: 646 sheet: 0.33 (0.31), residues: 270 loop : 0.06 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 413 HIS 0.005 0.001 HIS B 709 PHE 0.021 0.002 PHE A 218 TYR 0.018 0.002 TYR B 629 ARG 0.008 0.001 ARG B 690 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 172 time to evaluate : 1.735 Fit side-chains REVERT: A 196 LYS cc_start: 0.8543 (ttmm) cc_final: 0.8225 (ttmm) REVERT: A 225 GLU cc_start: 0.6740 (tm-30) cc_final: 0.5877 (tm-30) REVERT: A 229 ARG cc_start: 0.8150 (ttp-170) cc_final: 0.7637 (ptt90) REVERT: A 548 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6532 (mt-10) REVERT: A 780 LYS cc_start: 0.7622 (mttt) cc_final: 0.7262 (mmtt) REVERT: B 229 ARG cc_start: 0.7551 (ptt90) cc_final: 0.7073 (ptt90) REVERT: B 233 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7489 (pm20) REVERT: B 314 MET cc_start: 0.8363 (mtt) cc_final: 0.8015 (mtm) REVERT: B 548 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6738 (mt-10) outliers start: 23 outliers final: 16 residues processed: 186 average time/residue: 0.2830 time to fit residues: 74.9314 Evaluate side-chains 180 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 161 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 882 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 chunk 109 optimal weight: 7.9990 chunk 0 optimal weight: 1.9990 chunk 80 optimal weight: 0.1980 chunk 142 optimal weight: 0.5980 chunk 40 optimal weight: 0.0770 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 592 ASN B 706 GLN ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 848 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13610 Z= 0.156 Angle : 0.469 7.412 18374 Z= 0.240 Chirality : 0.041 0.137 2018 Planarity : 0.004 0.036 2360 Dihedral : 3.747 17.105 1824 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.42 % Allowed : 9.89 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.21), residues: 1638 helix: 1.41 (0.20), residues: 652 sheet: 0.37 (0.31), residues: 270 loop : 0.29 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 413 HIS 0.002 0.000 HIS A 625 PHE 0.012 0.001 PHE A 218 TYR 0.011 0.001 TYR B 629 ARG 0.009 0.000 ARG B 690 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 163 time to evaluate : 1.589 Fit side-chains revert: symmetry clash REVERT: A 780 LYS cc_start: 0.7560 (mttt) cc_final: 0.7284 (mmtt) REVERT: B 229 ARG cc_start: 0.7485 (ptt90) cc_final: 0.6997 (ptt90) REVERT: B 233 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7518 (pm20) outliers start: 21 outliers final: 14 residues processed: 172 average time/residue: 0.2816 time to fit residues: 69.3577 Evaluate side-chains 173 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 158 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 840 ASP Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 882 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 2.9990 chunk 142 optimal weight: 0.5980 chunk 31 optimal weight: 0.0980 chunk 93 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 158 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 73 optimal weight: 0.0770 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 ASN ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 848 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13610 Z= 0.160 Angle : 0.464 7.787 18374 Z= 0.235 Chirality : 0.041 0.140 2018 Planarity : 0.003 0.039 2360 Dihedral : 3.625 16.507 1824 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.83 % Allowed : 9.42 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.21), residues: 1638 helix: 1.55 (0.21), residues: 652 sheet: 0.39 (0.31), residues: 270 loop : 0.35 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 413 HIS 0.003 0.001 HIS A 848 PHE 0.011 0.001 PHE A 218 TYR 0.012 0.001 TYR B 629 ARG 0.010 0.000 ARG B 690 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 164 time to evaluate : 1.696 Fit side-chains REVERT: A 217 GLN cc_start: 0.7182 (tp-100) cc_final: 0.6968 (tp40) REVERT: A 225 GLU cc_start: 0.6652 (tm-30) cc_final: 0.4993 (tm-30) REVERT: A 229 ARG cc_start: 0.8025 (ttp-170) cc_final: 0.7603 (ptt90) REVERT: A 478 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6968 (pm20) REVERT: A 676 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6896 (mp0) REVERT: A 780 LYS cc_start: 0.7530 (mttt) cc_final: 0.7255 (mmtt) REVERT: A 852 ASP cc_start: 0.7383 (t0) cc_final: 0.7157 (m-30) REVERT: B 217 GLN cc_start: 0.7172 (OUTLIER) cc_final: 0.6940 (tp-100) REVERT: B 229 ARG cc_start: 0.7484 (ptt90) cc_final: 0.7024 (ptt90) REVERT: B 233 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7525 (pm20) REVERT: B 272 ARG cc_start: 0.7861 (ptm160) cc_final: 0.7510 (mtp180) REVERT: B 548 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6683 (mt-10) outliers start: 27 outliers final: 18 residues processed: 180 average time/residue: 0.3004 time to fit residues: 77.3338 Evaluate side-chains 182 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 159 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 840 ASP Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 882 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 158 optimal weight: 0.4980 chunk 98 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 ASN ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 848 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13610 Z= 0.220 Angle : 0.485 6.633 18374 Z= 0.246 Chirality : 0.042 0.147 2018 Planarity : 0.004 0.044 2360 Dihedral : 3.668 16.887 1824 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.03 % Allowed : 9.89 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.21), residues: 1638 helix: 1.47 (0.20), residues: 654 sheet: 0.37 (0.31), residues: 270 loop : 0.29 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 413 HIS 0.002 0.001 HIS B 709 PHE 0.012 0.001 PHE A 218 TYR 0.013 0.001 TYR B 629 ARG 0.011 0.000 ARG B 690 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 165 time to evaluate : 1.590 Fit side-chains REVERT: A 225 GLU cc_start: 0.6701 (tm-30) cc_final: 0.5236 (tm-30) REVERT: A 229 ARG cc_start: 0.8066 (ttp-170) cc_final: 0.7597 (ptt90) REVERT: A 478 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6994 (pm20) REVERT: A 548 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6535 (mt-10) REVERT: A 676 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: A 780 LYS cc_start: 0.7575 (mttt) cc_final: 0.7286 (mmtt) REVERT: B 217 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.6939 (tp-100) REVERT: B 233 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7565 (pm20) REVERT: B 272 ARG cc_start: 0.7860 (ptm160) cc_final: 0.7434 (mtp180) REVERT: B 548 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6685 (mt-10) REVERT: B 725 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7125 (tp30) REVERT: B 729 ARG cc_start: 0.7590 (mmt90) cc_final: 0.7349 (mtt-85) outliers start: 30 outliers final: 21 residues processed: 183 average time/residue: 0.2934 time to fit residues: 76.2725 Evaluate side-chains 191 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 164 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 840 ASP Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 877 ILE Chi-restraints excluded: chain B residue 882 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 107 optimal weight: 0.0000 chunk 78 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 638 ASN ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 848 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13610 Z= 0.237 Angle : 0.495 6.735 18374 Z= 0.251 Chirality : 0.042 0.137 2018 Planarity : 0.004 0.040 2360 Dihedral : 3.724 17.289 1824 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.96 % Allowed : 10.23 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.21), residues: 1638 helix: 1.45 (0.20), residues: 652 sheet: 0.32 (0.31), residues: 270 loop : 0.29 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 413 HIS 0.002 0.001 HIS B 709 PHE 0.011 0.001 PHE A 218 TYR 0.014 0.001 TYR B 629 ARG 0.010 0.000 ARG B 690 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 165 time to evaluate : 1.651 Fit side-chains REVERT: A 225 GLU cc_start: 0.6770 (tm-30) cc_final: 0.5814 (tm-30) REVERT: A 229 ARG cc_start: 0.8045 (ttp-170) cc_final: 0.7567 (ptt90) REVERT: A 478 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7028 (pm20) REVERT: A 548 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.6542 (mt-10) REVERT: A 676 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6867 (mp0) REVERT: A 780 LYS cc_start: 0.7561 (mttt) cc_final: 0.7272 (mmtt) REVERT: A 830 MET cc_start: 0.7063 (ttm) cc_final: 0.6788 (ttm) REVERT: A 852 ASP cc_start: 0.7457 (t0) cc_final: 0.7177 (m-30) REVERT: B 217 GLN cc_start: 0.7136 (OUTLIER) cc_final: 0.6920 (tp-100) REVERT: B 229 ARG cc_start: 0.7441 (ptt90) cc_final: 0.6860 (ptt-90) REVERT: B 233 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7582 (pm20) REVERT: B 272 ARG cc_start: 0.7814 (ptm160) cc_final: 0.7391 (mtp180) REVERT: B 382 TYR cc_start: 0.7917 (m-10) cc_final: 0.7688 (m-80) REVERT: B 548 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6735 (mt-10) REVERT: B 725 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6980 (tp30) REVERT: B 729 ARG cc_start: 0.7640 (mmt90) cc_final: 0.7400 (mtt-85) outliers start: 29 outliers final: 21 residues processed: 183 average time/residue: 0.2937 time to fit residues: 76.1231 Evaluate side-chains 189 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 162 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 840 ASP Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 877 ILE Chi-restraints excluded: chain B residue 882 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 4.9990 chunk 151 optimal weight: 0.0010 chunk 138 optimal weight: 0.5980 chunk 147 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 45 optimal weight: 0.0000 chunk 133 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 848 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13610 Z= 0.147 Angle : 0.465 6.595 18374 Z= 0.235 Chirality : 0.041 0.166 2018 Planarity : 0.003 0.036 2360 Dihedral : 3.561 16.118 1824 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.63 % Allowed : 10.84 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.21), residues: 1638 helix: 1.66 (0.21), residues: 652 sheet: 0.41 (0.31), residues: 270 loop : 0.37 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 413 HIS 0.002 0.000 HIS A 848 PHE 0.010 0.001 PHE A 218 TYR 0.013 0.001 TYR B 824 ARG 0.009 0.000 ARG B 690 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 162 time to evaluate : 1.610 Fit side-chains REVERT: A 478 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6969 (pm20) REVERT: A 553 SER cc_start: 0.7899 (m) cc_final: 0.7690 (p) REVERT: A 676 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6847 (mp0) REVERT: A 780 LYS cc_start: 0.7505 (mttt) cc_final: 0.7228 (mmtt) REVERT: A 830 MET cc_start: 0.7014 (ttm) cc_final: 0.6771 (ttm) REVERT: B 229 ARG cc_start: 0.7397 (ptt90) cc_final: 0.6829 (ptt-90) REVERT: B 233 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7548 (pm20) REVERT: B 272 ARG cc_start: 0.7809 (ptm160) cc_final: 0.7381 (mtp180) REVERT: B 548 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6671 (mt-10) outliers start: 24 outliers final: 17 residues processed: 175 average time/residue: 0.2862 time to fit residues: 71.7140 Evaluate side-chains 174 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 153 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 840 ASP Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 882 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 163 optimal weight: 0.7980 chunk 150 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 100 optimal weight: 0.4980 chunk 79 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 ASN A 661 HIS ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 848 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13610 Z= 0.223 Angle : 0.495 6.736 18374 Z= 0.251 Chirality : 0.042 0.159 2018 Planarity : 0.004 0.036 2360 Dihedral : 3.621 16.864 1824 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.69 % Allowed : 11.11 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.21), residues: 1638 helix: 1.57 (0.20), residues: 652 sheet: 0.38 (0.31), residues: 270 loop : 0.33 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 413 HIS 0.006 0.001 HIS A 625 PHE 0.011 0.001 PHE A 218 TYR 0.013 0.001 TYR B 629 ARG 0.009 0.000 ARG B 690 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 164 time to evaluate : 1.710 Fit side-chains revert: symmetry clash REVERT: A 478 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7011 (pm20) REVERT: A 548 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6566 (mt-10) REVERT: A 676 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6846 (mp0) REVERT: A 780 LYS cc_start: 0.7529 (mttt) cc_final: 0.7240 (mmtt) REVERT: A 822 TYR cc_start: 0.6871 (m-80) cc_final: 0.6521 (m-80) REVERT: A 830 MET cc_start: 0.7036 (ttm) cc_final: 0.6792 (ttm) REVERT: B 229 ARG cc_start: 0.7465 (ptt90) cc_final: 0.6903 (ptt-90) REVERT: B 233 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7580 (pm20) REVERT: B 272 ARG cc_start: 0.7823 (ptm160) cc_final: 0.7396 (mtp180) REVERT: B 548 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6735 (mt-10) REVERT: B 725 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6966 (tp30) outliers start: 25 outliers final: 19 residues processed: 178 average time/residue: 0.2920 time to fit residues: 73.8350 Evaluate side-chains 185 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 161 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 840 ASP Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 882 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 19 optimal weight: 0.0770 chunk 36 optimal weight: 0.6980 chunk 130 optimal weight: 0.0980 chunk 54 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 638 ASN ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 848 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.165828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.124678 restraints weight = 14837.446| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.45 r_work: 0.3262 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13610 Z= 0.157 Angle : 0.472 6.728 18374 Z= 0.239 Chirality : 0.041 0.155 2018 Planarity : 0.003 0.034 2360 Dihedral : 3.557 16.143 1824 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.76 % Allowed : 10.91 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.21), residues: 1638 helix: 1.68 (0.21), residues: 652 sheet: 0.42 (0.31), residues: 270 loop : 0.37 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 413 HIS 0.005 0.001 HIS A 625 PHE 0.010 0.001 PHE A 207 TYR 0.011 0.001 TYR B 629 ARG 0.009 0.000 ARG B 690 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2943.94 seconds wall clock time: 54 minutes 27.69 seconds (3267.69 seconds total)