Starting phenix.real_space_refine on Sat Nov 16 21:52:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hke_34850/11_2024/8hke_34850.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hke_34850/11_2024/8hke_34850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hke_34850/11_2024/8hke_34850.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hke_34850/11_2024/8hke_34850.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hke_34850/11_2024/8hke_34850.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hke_34850/11_2024/8hke_34850.cif" } resolution = 3.71 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= 0.002 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 74 5.49 5 S 66 5.16 5 C 7400 2.51 5 N 1983 2.21 5 O 2329 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 11854 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 5089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5089 Classifications: {'peptide': 647} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 629} Chain breaks: 3 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 8, 'ASN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "A" Number of atoms: 5189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5189 Classifications: {'peptide': 659} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 640} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 8, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 53 Chain: "C" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 790 Classifications: {'RNA': 37} Modifications used: {'rna3p_pur': 20, 'rna3p_pyr': 17} Link IDs: {'rna3p': 36} Chain: "D" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 784 Classifications: {'RNA': 37} Modifications used: {'rna3p_pur': 17, 'rna3p_pyr': 20} Link IDs: {'rna3p': 36} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.46, per 1000 atoms: 0.63 Number of scatterers: 11854 At special positions: 0 Unit cell: (116.48, 112.32, 132.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 66 16.00 P 74 15.00 O 2329 8.00 N 1983 7.00 C 7400 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 225 " - pdb=" SG CYS B 287 " distance=2.03 Simple disulfide: pdb=" SG CYS B 464 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 225 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 731 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 540 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 740 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 744 " pdb=" ZN B 801 " pdb="ZN ZN B 801 " - pdb=" NE2 HIS B 540 " pdb="ZN ZN B 801 " - pdb=" NE2 HIS B 744 " pdb="ZN ZN B 801 " - pdb=" NE2 HIS B 740 " 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2508 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 11 sheets defined 46.1% alpha, 10.5% beta 24 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'B' and resid 80 through 85 Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 205 through 210 Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 264 through 272 removed outlier: 4.084A pdb=" N MET B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 323 Processing helix chain 'B' and resid 327 through 332 removed outlier: 4.118A pdb=" N LEU B 331 " --> pdb=" O PRO B 328 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE B 332 " --> pdb=" O CYS B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 344 removed outlier: 3.658A pdb=" N ILE B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS B 341 " --> pdb=" O ILE B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 433 removed outlier: 3.603A pdb=" N MET B 430 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU B 431 " --> pdb=" O HIS B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 444 through 454 removed outlier: 3.755A pdb=" N HIS B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP B 452 " --> pdb=" O GLU B 448 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR B 454 " --> pdb=" O HIS B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 464 removed outlier: 3.714A pdb=" N CYS B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 485 No H-bonds generated for 'chain 'B' and resid 483 through 485' Processing helix chain 'B' and resid 486 through 502 removed outlier: 4.143A pdb=" N THR B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA B 494 " --> pdb=" O THR B 490 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE B 496 " --> pdb=" O TYR B 492 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 498 " --> pdb=" O ALA B 494 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE B 501 " --> pdb=" O ILE B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 531 removed outlier: 3.727A pdb=" N THR B 524 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY B 526 " --> pdb=" O ASP B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 540 removed outlier: 4.411A pdb=" N ALA B 537 " --> pdb=" O SER B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 569 removed outlier: 4.236A pdb=" N MET B 563 " --> pdb=" O CYS B 559 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN B 566 " --> pdb=" O LEU B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 577 No H-bonds generated for 'chain 'B' and resid 575 through 577' Processing helix chain 'B' and resid 578 through 596 removed outlier: 3.956A pdb=" N VAL B 584 " --> pdb=" O ASN B 580 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 585 " --> pdb=" O ILE B 581 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 626 removed outlier: 3.644A pdb=" N ILE B 605 " --> pdb=" O TYR B 601 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA B 607 " --> pdb=" O ARG B 603 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N HIS B 610 " --> pdb=" O ILE B 606 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS B 621 " --> pdb=" O ILE B 617 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU B 622 " --> pdb=" O CYS B 618 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER B 624 " --> pdb=" O ALA B 620 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B 626 " --> pdb=" O GLU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 652 removed outlier: 3.783A pdb=" N PHE B 639 " --> pdb=" O PHE B 635 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE B 644 " --> pdb=" O SER B 640 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET B 649 " --> pdb=" O ALA B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 684 removed outlier: 4.458A pdb=" N THR B 663 " --> pdb=" O ASN B 659 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR B 677 " --> pdb=" O TYR B 673 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL B 682 " --> pdb=" O GLY B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 709 removed outlier: 3.778A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 713 Processing helix chain 'B' and resid 722 through 727 removed outlier: 3.622A pdb=" N LEU B 727 " --> pdb=" O ALA B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 761 removed outlier: 3.581A pdb=" N TRP B 743 " --> pdb=" O SER B 739 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS B 744 " --> pdb=" O HIS B 740 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE B 745 " --> pdb=" O ASP B 741 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA B 748 " --> pdb=" O HIS B 744 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE B 755 " --> pdb=" O GLY B 751 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N VAL B 758 " --> pdb=" O THR B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 768 removed outlier: 3.860A pdb=" N ASN B 767 " --> pdb=" O ASP B 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 68 removed outlier: 3.713A pdb=" N ILE A 68 " --> pdb=" O GLN A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 85 Processing helix chain 'A' and resid 128 through 132 removed outlier: 3.982A pdb=" N PHE A 131 " --> pdb=" O GLU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 210 removed outlier: 3.731A pdb=" N ASN A 210 " --> pdb=" O SER A 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 210' Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 314 through 325 removed outlier: 3.696A pdb=" N THR A 318 " --> pdb=" O TYR A 314 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 320 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET A 321 " --> pdb=" O PRO A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 341 through 344 Processing helix chain 'A' and resid 426 through 433 Processing helix chain 'A' and resid 438 through 454 Processing helix chain 'A' and resid 458 through 464 Processing helix chain 'A' and resid 480 through 485 Processing helix chain 'A' and resid 486 through 493 removed outlier: 3.683A pdb=" N THR A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 503 removed outlier: 4.193A pdb=" N ILE A 501 " --> pdb=" O ILE A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 540 removed outlier: 3.692A pdb=" N SER A 533 " --> pdb=" O MET A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 569 removed outlier: 4.158A pdb=" N MET A 563 " --> pdb=" O CYS A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 596 removed outlier: 4.199A pdb=" N ILE A 581 " --> pdb=" O ALA A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 626 removed outlier: 3.547A pdb=" N SER A 624 " --> pdb=" O ALA A 620 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A 625 " --> pdb=" O LYS A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 652 removed outlier: 4.032A pdb=" N MET A 637 " --> pdb=" O ARG A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 684 removed outlier: 3.619A pdb=" N ILE A 661 " --> pdb=" O HIS A 657 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ALA A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR A 663 " --> pdb=" O ASN A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 711 Processing helix chain 'A' and resid 720 through 726 Processing helix chain 'A' and resid 739 through 759 removed outlier: 3.609A pdb=" N ALA A 748 " --> pdb=" O HIS A 744 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 35 through 39 removed outlier: 3.531A pdb=" N VAL B 151 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR B 152 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN B 154 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU B 93 " --> pdb=" O GLN B 154 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 4.255A pdb=" N ARG B 164 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU B 77 " --> pdb=" O ARG B 164 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 186 through 193 removed outlier: 5.693A pdb=" N THR B 188 " --> pdb=" O PHE B 306 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N PHE B 306 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N SER B 190 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N PHE B 304 " --> pdb=" O SER B 190 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 200 through 204 removed outlier: 3.544A pdb=" N ILE B 200 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN B 227 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B 230 " --> pdb=" O ARG B 251 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 251 " --> pdb=" O THR B 230 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 36 through 39 removed outlier: 3.796A pdb=" N VAL A 58 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A 152 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 47 through 51 removed outlier: 3.656A pdb=" N LYS A 49 " --> pdb=" O TYR A 163 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR A 163 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.606A pdb=" N LYS A 73 " --> pdb=" O THR A 168 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA9, first strand: chain 'A' and resid 186 through 187 removed outlier: 3.805A pdb=" N GLN A 213 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 200 through 201 Processing sheet with id=AB2, first strand: chain 'A' and resid 200 through 201 removed outlier: 3.572A pdb=" N ASN A 227 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE A 255 " --> pdb=" O ALA A 226 " (cutoff:3.500A) 431 hydrogen bonds defined for protein. 1179 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 58 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 4.82 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3281 1.33 - 1.45: 2716 1.45 - 1.57: 6027 1.57 - 1.69: 146 1.69 - 1.81: 98 Bond restraints: 12268 Sorted by residual: bond pdb=" CA TYR B 492 " pdb=" C TYR B 492 " ideal model delta sigma weight residual 1.523 1.458 0.065 1.80e-02 3.09e+03 1.31e+01 bond pdb=" C PRO A 574 " pdb=" N SER A 575 " ideal model delta sigma weight residual 1.331 1.256 0.075 2.07e-02 2.33e+03 1.30e+01 bond pdb=" C GLU A 93 " pdb=" N VAL A 94 " ideal model delta sigma weight residual 1.330 1.300 0.031 1.48e-02 4.57e+03 4.28e+00 bond pdb=" CA VAL A 278 " pdb=" C VAL A 278 " ideal model delta sigma weight residual 1.527 1.509 0.018 8.50e-03 1.38e+04 4.25e+00 bond pdb=" CA SER B 269 " pdb=" C SER B 269 " ideal model delta sigma weight residual 1.523 1.490 0.033 1.80e-02 3.09e+03 3.41e+00 ... (remaining 12263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.96: 16946 4.96 - 9.92: 34 9.92 - 14.88: 4 14.88 - 19.84: 0 19.84 - 24.80: 2 Bond angle restraints: 16986 Sorted by residual: angle pdb=" C ASN A 234 " pdb=" CA ASN A 234 " pdb=" CB ASN A 234 " ideal model delta sigma weight residual 110.81 135.61 -24.80 1.60e+00 3.91e-01 2.40e+02 angle pdb=" N ALA A 469 " pdb=" CA ALA A 469 " pdb=" C ALA A 469 " ideal model delta sigma weight residual 110.80 90.59 20.21 2.13e+00 2.20e-01 9.01e+01 angle pdb=" C PRO B 553 " pdb=" CA PRO B 553 " pdb=" CB PRO B 553 " ideal model delta sigma weight residual 111.56 125.99 -14.43 1.65e+00 3.67e-01 7.64e+01 angle pdb=" N SER A 66 " pdb=" CA SER A 66 " pdb=" C SER A 66 " ideal model delta sigma weight residual 113.01 122.68 -9.67 1.20e+00 6.94e-01 6.50e+01 angle pdb=" C HIS A 468 " pdb=" CA HIS A 468 " pdb=" CB HIS A 468 " ideal model delta sigma weight residual 111.83 100.42 11.41 1.60e+00 3.91e-01 5.09e+01 ... (remaining 16981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 6465 17.99 - 35.98: 637 35.98 - 53.97: 136 53.97 - 71.95: 105 71.95 - 89.94: 27 Dihedral angle restraints: 7370 sinusoidal: 3523 harmonic: 3847 Sorted by residual: dihedral pdb=" C ASN A 234 " pdb=" N ASN A 234 " pdb=" CA ASN A 234 " pdb=" CB ASN A 234 " ideal model delta harmonic sigma weight residual -122.60 -153.92 31.32 0 2.50e+00 1.60e-01 1.57e+02 dihedral pdb=" CB CYS A 470 " pdb=" SG CYS A 470 " pdb=" SG CYS A 731 " pdb=" CB CYS A 731 " ideal model delta sinusoidal sigma weight residual -86.00 -163.25 77.25 1 1.00e+01 1.00e-02 7.48e+01 dihedral pdb=" N ASN A 234 " pdb=" C ASN A 234 " pdb=" CA ASN A 234 " pdb=" CB ASN A 234 " ideal model delta harmonic sigma weight residual 122.80 144.03 -21.23 0 2.50e+00 1.60e-01 7.21e+01 ... (remaining 7367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.234: 2047 0.234 - 0.467: 2 0.467 - 0.701: 2 0.701 - 0.934: 0 0.934 - 1.168: 1 Chirality restraints: 2052 Sorted by residual: chirality pdb=" CA ASN A 234 " pdb=" N ASN A 234 " pdb=" C ASN A 234 " pdb=" CB ASN A 234 " both_signs ideal model delta sigma weight residual False 2.51 1.34 1.17 2.00e-01 2.50e+01 3.41e+01 chirality pdb=" CA PRO B 553 " pdb=" N PRO B 553 " pdb=" C PRO B 553 " pdb=" CB PRO B 553 " both_signs ideal model delta sigma weight residual False 2.72 2.15 0.57 2.00e-01 2.50e+01 8.01e+00 chirality pdb=" CA HIS A 468 " pdb=" N HIS A 468 " pdb=" C HIS A 468 " pdb=" CB HIS A 468 " both_signs ideal model delta sigma weight residual False 2.51 3.06 -0.55 2.00e-01 2.50e+01 7.62e+00 ... (remaining 2049 not shown) Planarity restraints: 1837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G D 12 " 0.032 2.00e-02 2.50e+03 1.39e-02 5.80e+00 pdb=" N9 G D 12 " -0.031 2.00e-02 2.50e+03 pdb=" C8 G D 12 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G D 12 " 0.004 2.00e-02 2.50e+03 pdb=" C5 G D 12 " -0.004 2.00e-02 2.50e+03 pdb=" C6 G D 12 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G D 12 " 0.008 2.00e-02 2.50e+03 pdb=" N1 G D 12 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G D 12 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G D 12 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G D 12 " -0.012 2.00e-02 2.50e+03 pdb=" C4 G D 12 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 542 " 0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO A 543 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 543 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 543 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C D 13 " 0.024 2.00e-02 2.50e+03 1.35e-02 4.09e+00 pdb=" N1 C D 13 " -0.032 2.00e-02 2.50e+03 pdb=" C2 C D 13 " -0.003 2.00e-02 2.50e+03 pdb=" O2 C D 13 " -0.000 2.00e-02 2.50e+03 pdb=" N3 C D 13 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C D 13 " -0.000 2.00e-02 2.50e+03 pdb=" N4 C D 13 " 0.007 2.00e-02 2.50e+03 pdb=" C5 C D 13 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C D 13 " -0.000 2.00e-02 2.50e+03 ... (remaining 1834 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 212 2.62 - 3.19: 11379 3.19 - 3.76: 18463 3.76 - 4.33: 25886 4.33 - 4.90: 40241 Nonbonded interactions: 96181 Sorted by model distance: nonbonded pdb=" NZ LYS A 45 " pdb=" OP1 U D 25 " model vdw 2.049 3.120 nonbonded pdb=" OD2 ASP B 551 " pdb="ZN ZN B 801 " model vdw 2.077 2.230 nonbonded pdb=" NZ LYS A 299 " pdb=" OP2 C C 19 " model vdw 2.141 3.120 nonbonded pdb=" O ILE B 606 " pdb=" OH TYR B 650 " model vdw 2.157 3.040 nonbonded pdb=" OG1 THR A 515 " pdb=" O VAL A 569 " model vdw 2.158 3.040 ... (remaining 96176 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 34 through 131 or resid 144 through 170 or (resid 171 thro \ ugh 173 and (name N or name CA or name C or name O or name CB )) or resid 174 th \ rough 292 or (resid 293 through 294 and (name N or name CA or name C or name O o \ r name CB )) or resid 295 through 296 or (resid 297 through 299 and (name N or n \ ame CA or name C or name O or name CB )) or resid 300 through 776 or resid 801)) \ 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 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: 0.890 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: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 33.700 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 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 : 0.007 0.075 12268 Z= 0.483 Angle : 0.823 24.798 16986 Z= 0.449 Chirality : 0.057 1.168 2052 Planarity : 0.004 0.056 1837 Dihedral : 17.029 89.943 4847 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 0.09 % Allowed : 9.10 % Favored : 90.81 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -5.00 (0.19), residues: 1292 helix: -3.04 (0.17), residues: 513 sheet: -3.93 (0.28), residues: 230 loop : -3.12 (0.24), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 452 HIS 0.008 0.002 HIS A 744 PHE 0.033 0.002 PHE A 639 TYR 0.020 0.002 TYR A 650 ARG 0.004 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7679 (mt-10) REVERT: B 484 ILE cc_start: 0.9276 (tp) cc_final: 0.8861 (tp) REVERT: B 591 PHE cc_start: 0.8249 (t80) cc_final: 0.8016 (t80) REVERT: A 106 LYS cc_start: 0.8704 (mttt) cc_final: 0.8172 (mtmt) REVERT: A 219 TYR cc_start: 0.8276 (m-80) cc_final: 0.7847 (m-80) REVERT: A 314 TYR cc_start: 0.8733 (m-80) cc_final: 0.8473 (m-80) REVERT: A 637 MET cc_start: 0.7661 (ttp) cc_final: 0.6338 (tmm) REVERT: A 641 MET cc_start: 0.5650 (ptt) cc_final: 0.5204 (ptt) REVERT: A 681 LYS cc_start: 0.9091 (tttp) cc_final: 0.8851 (tttt) REVERT: A 728 ASN cc_start: 0.8183 (p0) cc_final: 0.7608 (p0) REVERT: A 741 ASP cc_start: 0.7995 (m-30) cc_final: 0.7717 (m-30) outliers start: 1 outliers final: 1 residues processed: 201 average time/residue: 0.2463 time to fit residues: 70.5062 Evaluate side-chains 151 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 122 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN B 113 ASN B 566 GLN ** B 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 GLN A 432 GLN A 444 HIS A 566 GLN A 590 ASN A 643 ASN A 657 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12268 Z= 0.193 Angle : 0.609 8.245 16986 Z= 0.312 Chirality : 0.042 0.159 2052 Planarity : 0.004 0.048 1837 Dihedral : 17.345 92.931 2543 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.34 % Allowed : 14.01 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -3.13 (0.22), residues: 1292 helix: -1.11 (0.21), residues: 527 sheet: -3.30 (0.29), residues: 243 loop : -2.30 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 567 HIS 0.006 0.001 HIS B 166 PHE 0.026 0.001 PHE B 324 TYR 0.024 0.001 TYR A 650 ARG 0.007 0.001 ARG B 769 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7413 (pm20) REVERT: B 322 MET cc_start: 0.8182 (mmt) cc_final: 0.7958 (mmt) REVERT: B 484 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8874 (tp) REVERT: B 563 MET cc_start: 0.7279 (mtt) cc_final: 0.6781 (mmm) REVERT: A 193 LYS cc_start: 0.9168 (tptt) cc_final: 0.8937 (tttp) REVERT: A 219 TYR cc_start: 0.8090 (m-80) cc_final: 0.7587 (m-10) REVERT: A 261 ILE cc_start: 0.9167 (mt) cc_final: 0.8912 (mm) REVERT: A 484 ILE cc_start: 0.9179 (tp) cc_final: 0.8613 (tp) REVERT: A 637 MET cc_start: 0.7325 (ttp) cc_final: 0.6139 (tmm) REVERT: A 641 MET cc_start: 0.5235 (ptt) cc_final: 0.4827 (ptt) REVERT: A 681 LYS cc_start: 0.9006 (tttp) cc_final: 0.8077 (tttt) REVERT: A 728 ASN cc_start: 0.8128 (p0) cc_final: 0.7568 (p0) outliers start: 15 outliers final: 8 residues processed: 192 average time/residue: 0.1999 time to fit residues: 57.7762 Evaluate side-chains 151 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 731 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 132 optimal weight: 30.0000 chunk 109 optimal weight: 0.0980 chunk 121 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12268 Z= 0.346 Angle : 0.637 9.344 16986 Z= 0.324 Chirality : 0.043 0.154 2052 Planarity : 0.004 0.046 1837 Dihedral : 17.245 94.435 2543 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.48 % Allowed : 16.32 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -2.62 (0.23), residues: 1292 helix: -0.57 (0.22), residues: 541 sheet: -3.09 (0.29), residues: 243 loop : -2.19 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 452 HIS 0.006 0.001 HIS A 468 PHE 0.025 0.002 PHE A 131 TYR 0.022 0.001 TYR A 650 ARG 0.005 0.000 ARG B 504 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 461 ASP cc_start: 0.8445 (m-30) cc_final: 0.8013 (m-30) REVERT: B 484 ILE cc_start: 0.9085 (tp) cc_final: 0.8774 (tp) REVERT: B 487 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8476 (tp) REVERT: A 88 ASP cc_start: 0.7529 (p0) cc_final: 0.6982 (p0) REVERT: A 106 LYS cc_start: 0.8649 (mttt) cc_final: 0.8405 (mttm) REVERT: A 219 TYR cc_start: 0.8271 (m-80) cc_final: 0.7851 (m-10) REVERT: A 520 LEU cc_start: 0.8139 (mm) cc_final: 0.7830 (mt) REVERT: A 522 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8240 (t0) REVERT: A 637 MET cc_start: 0.7362 (ttp) cc_final: 0.7142 (tmm) REVERT: A 728 ASN cc_start: 0.8195 (p0) cc_final: 0.7612 (p0) outliers start: 39 outliers final: 27 residues processed: 180 average time/residue: 0.1991 time to fit residues: 55.9310 Evaluate side-chains 169 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 679 CYS Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 733 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 58 optimal weight: 0.0870 chunk 82 optimal weight: 0.8980 chunk 123 optimal weight: 0.1980 chunk 130 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 116 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 GLN A 166 HIS A 466 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12268 Z= 0.193 Angle : 0.545 9.579 16986 Z= 0.279 Chirality : 0.040 0.149 2052 Planarity : 0.003 0.044 1837 Dihedral : 16.903 90.669 2543 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.41 % Allowed : 19.80 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -2.05 (0.24), residues: 1292 helix: -0.16 (0.23), residues: 543 sheet: -2.72 (0.31), residues: 247 loop : -1.83 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 452 HIS 0.005 0.001 HIS B 610 PHE 0.031 0.001 PHE B 324 TYR 0.024 0.001 TYR A 650 ARG 0.005 0.000 ARG B 504 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7696 (p0) cc_final: 0.7156 (p0) REVERT: A 193 LYS cc_start: 0.9193 (tptt) cc_final: 0.8871 (tttt) REVERT: A 219 TYR cc_start: 0.8044 (m-80) cc_final: 0.7598 (m-10) REVERT: A 261 ILE cc_start: 0.9166 (mt) cc_final: 0.8929 (mm) REVERT: A 484 ILE cc_start: 0.8877 (tp) cc_final: 0.8461 (tp) REVERT: A 520 LEU cc_start: 0.8103 (mm) cc_final: 0.7828 (mt) REVERT: A 522 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8147 (t0) REVERT: A 533 SER cc_start: 0.8759 (t) cc_final: 0.8446 (t) REVERT: A 637 MET cc_start: 0.7347 (ttp) cc_final: 0.6667 (ptt) REVERT: A 728 ASN cc_start: 0.8206 (p0) cc_final: 0.7661 (p0) outliers start: 27 outliers final: 16 residues processed: 178 average time/residue: 0.1975 time to fit residues: 54.6397 Evaluate side-chains 164 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 731 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 0.9980 chunk 74 optimal weight: 0.0370 chunk 1 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 117 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 overall best weight: 1.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN ** B 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 ASN ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12268 Z= 0.215 Angle : 0.557 9.998 16986 Z= 0.280 Chirality : 0.040 0.161 2052 Planarity : 0.003 0.042 1837 Dihedral : 16.654 85.139 2543 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.21 % Allowed : 19.80 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.73 (0.24), residues: 1292 helix: 0.12 (0.23), residues: 536 sheet: -2.50 (0.31), residues: 250 loop : -1.67 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 452 HIS 0.005 0.001 HIS B 610 PHE 0.022 0.001 PHE B 324 TYR 0.023 0.001 TYR A 650 ARG 0.004 0.000 ARG B 504 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 563 MET cc_start: 0.7541 (mtm) cc_final: 0.6032 (tmm) REVERT: A 88 ASP cc_start: 0.7672 (p0) cc_final: 0.7142 (p0) REVERT: A 193 LYS cc_start: 0.9164 (tptt) cc_final: 0.8861 (tttt) REVERT: A 219 TYR cc_start: 0.8099 (m-80) cc_final: 0.7660 (m-10) REVERT: A 261 ILE cc_start: 0.9222 (mt) cc_final: 0.8981 (mm) REVERT: A 484 ILE cc_start: 0.8872 (tp) cc_final: 0.8482 (tp) REVERT: A 520 LEU cc_start: 0.8155 (mm) cc_final: 0.7868 (mt) REVERT: A 522 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.8121 (t0) REVERT: A 533 SER cc_start: 0.8770 (t) cc_final: 0.8488 (t) REVERT: A 637 MET cc_start: 0.7294 (ttp) cc_final: 0.6602 (ptt) REVERT: A 681 LYS cc_start: 0.8725 (tttm) cc_final: 0.8394 (tttt) REVERT: A 728 ASN cc_start: 0.8203 (p0) cc_final: 0.7652 (p0) outliers start: 36 outliers final: 26 residues processed: 186 average time/residue: 0.2014 time to fit residues: 57.3368 Evaluate side-chains 177 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 733 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 4.9990 chunk 117 optimal weight: 0.0170 chunk 25 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 684 HIS A 148 ASN A 466 HIS ** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12268 Z= 0.191 Angle : 0.535 10.210 16986 Z= 0.270 Chirality : 0.039 0.160 2052 Planarity : 0.003 0.044 1837 Dihedral : 16.451 82.415 2543 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.57 % Allowed : 19.71 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.48 (0.24), residues: 1292 helix: 0.23 (0.23), residues: 542 sheet: -2.25 (0.33), residues: 241 loop : -1.54 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 452 HIS 0.006 0.001 HIS B 610 PHE 0.032 0.001 PHE A 708 TYR 0.024 0.001 TYR A 650 ARG 0.004 0.000 ARG B 504 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 167 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 484 ILE cc_start: 0.8769 (tp) cc_final: 0.8555 (tp) REVERT: B 676 TYR cc_start: 0.7533 (OUTLIER) cc_final: 0.6614 (t80) REVERT: B 680 MET cc_start: 0.8102 (mtp) cc_final: 0.7711 (mtp) REVERT: A 44 MET cc_start: 0.7499 (ppp) cc_final: 0.6953 (ppp) REVERT: A 80 ASP cc_start: 0.8004 (m-30) cc_final: 0.7559 (t0) REVERT: A 88 ASP cc_start: 0.7637 (p0) cc_final: 0.7108 (p0) REVERT: A 219 TYR cc_start: 0.8017 (m-80) cc_final: 0.7585 (m-80) REVERT: A 261 ILE cc_start: 0.9255 (mt) cc_final: 0.9014 (mm) REVERT: A 314 TYR cc_start: 0.8287 (m-80) cc_final: 0.7935 (m-80) REVERT: A 450 HIS cc_start: 0.7781 (OUTLIER) cc_final: 0.7236 (t70) REVERT: A 484 ILE cc_start: 0.8818 (tp) cc_final: 0.8397 (tp) REVERT: A 520 LEU cc_start: 0.8128 (mm) cc_final: 0.7749 (mt) REVERT: A 522 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8082 (t0) REVERT: A 533 SER cc_start: 0.8780 (t) cc_final: 0.8460 (t) REVERT: A 637 MET cc_start: 0.7270 (ttp) cc_final: 0.6587 (ptt) REVERT: A 649 MET cc_start: 0.7778 (mmm) cc_final: 0.7548 (mpp) REVERT: A 728 ASN cc_start: 0.8167 (p0) cc_final: 0.7622 (p0) outliers start: 40 outliers final: 26 residues processed: 195 average time/residue: 0.2016 time to fit residues: 60.7091 Evaluate side-chains 180 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 676 TYR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 450 HIS Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 731 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 109 optimal weight: 0.0060 chunk 72 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 81 optimal weight: 0.5980 chunk 79 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 overall best weight: 1.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 GLN ** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12268 Z= 0.231 Angle : 0.564 10.112 16986 Z= 0.283 Chirality : 0.040 0.165 2052 Planarity : 0.003 0.041 1837 Dihedral : 16.320 82.511 2541 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 4.64 % Allowed : 19.71 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.39 (0.24), residues: 1292 helix: 0.30 (0.23), residues: 543 sheet: -2.31 (0.32), residues: 249 loop : -1.40 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 452 HIS 0.006 0.001 HIS B 57 PHE 0.019 0.001 PHE A 131 TYR 0.022 0.001 TYR A 650 ARG 0.004 0.000 ARG B 478 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 156 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 LEU cc_start: 0.9021 (mt) cc_final: 0.8644 (tt) REVERT: B 260 ASP cc_start: 0.8676 (m-30) cc_final: 0.8377 (m-30) REVERT: B 676 TYR cc_start: 0.7590 (t80) cc_final: 0.6638 (t80) REVERT: B 680 MET cc_start: 0.8156 (mtp) cc_final: 0.7742 (mtp) REVERT: A 44 MET cc_start: 0.7386 (ppp) cc_final: 0.7169 (ppp) REVERT: A 88 ASP cc_start: 0.7641 (p0) cc_final: 0.7119 (p0) REVERT: A 193 LYS cc_start: 0.9073 (tptt) cc_final: 0.8790 (pttt) REVERT: A 219 TYR cc_start: 0.8073 (m-80) cc_final: 0.7691 (m-80) REVERT: A 450 HIS cc_start: 0.7783 (OUTLIER) cc_final: 0.7248 (t70) REVERT: A 484 ILE cc_start: 0.8831 (tp) cc_final: 0.8409 (tp) REVERT: A 487 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8032 (tp) REVERT: A 520 LEU cc_start: 0.8179 (mm) cc_final: 0.7876 (mt) REVERT: A 637 MET cc_start: 0.7253 (ttp) cc_final: 0.6528 (ptt) REVERT: A 728 ASN cc_start: 0.8207 (p0) cc_final: 0.7640 (p0) outliers start: 52 outliers final: 39 residues processed: 190 average time/residue: 0.2069 time to fit residues: 61.5772 Evaluate side-chains 192 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 450 HIS Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 731 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12268 Z= 0.197 Angle : 0.558 10.554 16986 Z= 0.279 Chirality : 0.040 0.172 2052 Planarity : 0.003 0.043 1837 Dihedral : 16.177 82.789 2541 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.57 % Allowed : 21.32 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.29 (0.24), residues: 1292 helix: 0.37 (0.23), residues: 542 sheet: -2.18 (0.32), residues: 247 loop : -1.38 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 452 HIS 0.006 0.001 HIS B 610 PHE 0.052 0.001 PHE A 496 TYR 0.022 0.001 TYR A 650 ARG 0.003 0.000 ARG B 504 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 LEU cc_start: 0.9005 (mt) cc_final: 0.8634 (tt) REVERT: B 260 ASP cc_start: 0.8731 (m-30) cc_final: 0.8426 (m-30) REVERT: B 676 TYR cc_start: 0.7540 (t80) cc_final: 0.6532 (t80) REVERT: B 680 MET cc_start: 0.8168 (mtp) cc_final: 0.7767 (mtp) REVERT: A 80 ASP cc_start: 0.7919 (m-30) cc_final: 0.7653 (t0) REVERT: A 88 ASP cc_start: 0.7575 (p0) cc_final: 0.7039 (p0) REVERT: A 168 THR cc_start: 0.9184 (p) cc_final: 0.8915 (t) REVERT: A 219 TYR cc_start: 0.7982 (m-80) cc_final: 0.7582 (m-80) REVERT: A 314 TYR cc_start: 0.8214 (m-80) cc_final: 0.7901 (m-80) REVERT: A 450 HIS cc_start: 0.7762 (OUTLIER) cc_final: 0.7197 (t70) REVERT: A 484 ILE cc_start: 0.8755 (tp) cc_final: 0.8367 (tp) REVERT: A 533 SER cc_start: 0.8792 (t) cc_final: 0.8472 (t) REVERT: A 637 MET cc_start: 0.7240 (ttp) cc_final: 0.6503 (ptt) REVERT: A 649 MET cc_start: 0.7779 (mmm) cc_final: 0.7531 (mpp) REVERT: A 728 ASN cc_start: 0.8170 (p0) cc_final: 0.7611 (p0) outliers start: 40 outliers final: 31 residues processed: 185 average time/residue: 0.1914 time to fit residues: 55.4642 Evaluate side-chains 187 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 450 HIS Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 731 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.9980 chunk 121 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12268 Z= 0.243 Angle : 0.577 14.478 16986 Z= 0.289 Chirality : 0.040 0.171 2052 Planarity : 0.003 0.040 1837 Dihedral : 16.134 83.075 2541 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.93 % Allowed : 21.23 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.23 (0.24), residues: 1292 helix: 0.37 (0.23), residues: 542 sheet: -2.11 (0.32), residues: 255 loop : -1.27 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 452 HIS 0.005 0.001 HIS B 610 PHE 0.062 0.002 PHE A 496 TYR 0.022 0.001 TYR A 650 ARG 0.003 0.000 ARG B 504 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 155 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 LEU cc_start: 0.9004 (mt) cc_final: 0.8640 (tt) REVERT: B 97 SER cc_start: 0.9186 (t) cc_final: 0.8859 (m) REVERT: B 100 ARG cc_start: 0.8040 (tpp80) cc_final: 0.7673 (tpp80) REVERT: B 260 ASP cc_start: 0.8750 (m-30) cc_final: 0.8464 (m-30) REVERT: B 676 TYR cc_start: 0.7644 (OUTLIER) cc_final: 0.6891 (t80) REVERT: B 680 MET cc_start: 0.8136 (mtp) cc_final: 0.7925 (mtp) REVERT: A 88 ASP cc_start: 0.7601 (p0) cc_final: 0.7053 (p0) REVERT: A 168 THR cc_start: 0.9208 (p) cc_final: 0.8957 (t) REVERT: A 193 LYS cc_start: 0.8937 (tptt) cc_final: 0.8678 (pttt) REVERT: A 219 TYR cc_start: 0.8079 (m-80) cc_final: 0.7689 (m-80) REVERT: A 314 TYR cc_start: 0.8257 (m-80) cc_final: 0.7924 (m-80) REVERT: A 450 HIS cc_start: 0.7795 (OUTLIER) cc_final: 0.7263 (t70) REVERT: A 484 ILE cc_start: 0.8803 (tp) cc_final: 0.8428 (tp) REVERT: A 520 LEU cc_start: 0.8173 (mm) cc_final: 0.7821 (mt) REVERT: A 637 MET cc_start: 0.7341 (ttp) cc_final: 0.6629 (ptt) REVERT: A 728 ASN cc_start: 0.8165 (p0) cc_final: 0.7581 (p0) outliers start: 44 outliers final: 37 residues processed: 186 average time/residue: 0.1869 time to fit residues: 53.9466 Evaluate side-chains 189 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 676 TYR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 450 HIS Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 731 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 123 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 82 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12268 Z= 0.248 Angle : 0.592 12.246 16986 Z= 0.298 Chirality : 0.040 0.262 2052 Planarity : 0.003 0.043 1837 Dihedral : 16.113 83.451 2541 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.30 % Allowed : 22.03 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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 (0.24), residues: 1292 helix: 0.35 (0.23), residues: 542 sheet: -2.05 (0.33), residues: 237 loop : -1.40 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 452 HIS 0.006 0.001 HIS B 540 PHE 0.067 0.001 PHE A 496 TYR 0.022 0.001 TYR A 650 ARG 0.003 0.000 ARG B 504 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 LEU cc_start: 0.9000 (mt) cc_final: 0.8644 (tt) REVERT: B 97 SER cc_start: 0.9186 (t) cc_final: 0.8913 (m) REVERT: B 100 ARG cc_start: 0.8079 (tpp80) cc_final: 0.7637 (tpp80) REVERT: B 260 ASP cc_start: 0.8744 (m-30) cc_final: 0.8479 (m-30) REVERT: B 676 TYR cc_start: 0.7607 (t80) cc_final: 0.6959 (t80) REVERT: A 88 ASP cc_start: 0.7452 (p0) cc_final: 0.6898 (p0) REVERT: A 168 THR cc_start: 0.9225 (p) cc_final: 0.8954 (t) REVERT: A 219 TYR cc_start: 0.8103 (m-80) cc_final: 0.7724 (m-10) REVERT: A 314 TYR cc_start: 0.8338 (m-80) cc_final: 0.7995 (m-80) REVERT: A 450 HIS cc_start: 0.7802 (OUTLIER) cc_final: 0.7271 (t70) REVERT: A 520 LEU cc_start: 0.8166 (mm) cc_final: 0.7828 (mt) REVERT: A 637 MET cc_start: 0.7357 (ttp) cc_final: 0.6627 (ptt) REVERT: A 728 ASN cc_start: 0.8142 (p0) cc_final: 0.7587 (p0) outliers start: 37 outliers final: 35 residues processed: 183 average time/residue: 0.1826 time to fit residues: 53.0251 Evaluate side-chains 188 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 450 HIS Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 731 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 15 optimal weight: 0.2980 chunk 29 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 ASN ** B 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 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 = 0.3956 r_free = 0.3956 target = 0.140691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.100822 restraints weight = 20704.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.103428 restraints weight = 12979.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.104903 restraints weight = 8825.793| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12268 Z= 0.196 Angle : 0.571 11.235 16986 Z= 0.287 Chirality : 0.040 0.272 2052 Planarity : 0.003 0.041 1837 Dihedral : 15.993 84.125 2541 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.21 % Allowed : 22.30 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.14 (0.24), residues: 1292 helix: 0.47 (0.23), residues: 536 sheet: -1.99 (0.33), residues: 245 loop : -1.31 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 452 HIS 0.006 0.001 HIS B 610 PHE 0.059 0.001 PHE A 496 TYR 0.035 0.001 TYR A 650 ARG 0.003 0.000 ARG B 504 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2175.92 seconds wall clock time: 41 minutes 3.52 seconds (2463.52 seconds total)