Starting phenix.real_space_refine on Wed Aug 5 22:35:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hke_34850/08_2026/8hke_34850.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hke_34850/08_2026/8hke_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8hke_34850/08_2026/8hke_34850.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hke_34850/08_2026/8hke_34850.cif" model { file = "/net/cci-nas-00/data/ceres_data/8hke_34850/08_2026/8hke_34850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hke_34850/08_2026/8hke_34850.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hke_34850/08_2026/8hke_34850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hke_34850/08_2026/8hke_34850.map" } resolution = 3.71 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/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: {'HIS:plan': 1, 'ASP:plan': 8, 'ARG:plan': 3, 'ASN:plan1': 1, 'GLU: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: {'HIS:plan': 3, 'ARG:plan': 2, 'ASP:plan': 8, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "C" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 790 Classifications: {'RNAv2': 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: {'RNAv2': 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: 2.68, per 1000 atoms: 0.23 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: 1.00 Conformation dependent library (CDL) restraints added in 568.9 milliseconds 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: 1.18 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: 2.09 Time building geometry restraints manager: 1.36 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: 16944 4.96 - 9.92: 36 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: 6393 17.99 - 35.98: 628 35.98 - 53.97: 157 53.97 - 71.95: 100 71.95 - 89.94: 24 Dihedral angle restraints: 7302 sinusoidal: 3455 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 7299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.234: 2019 0.234 - 0.467: 30 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 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: 1.500 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.750 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 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 : 0.008 0.188 12279 Z= 0.342 Angle : 0.872 24.798 16996 Z= 0.452 Chirality : 0.071 1.168 2052 Planarity : 0.004 0.056 1837 Dihedral : 17.191 89.943 4779 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 16.48 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.000 ARG A 135 TYR 0.020 0.002 TYR A 650 PHE 0.033 0.002 PHE A 639 TRP 0.020 0.002 TRP A 452 HIS 0.008 0.002 HIS A 744 Details of bonding type rmsd/Z covalent geometry : bond 0.00736 / 0.33 (12268) covalent geometry : angle 0.86984 / 0.45 (16986) SS BOND : bond 0.00466 / 0.29 ( 5) SS BOND : angle 2.84565 / 1.37 ( 10) hydrogen bonds : bond 0.23477 / 15.37 ( 487) hydrogen bonds : angle 9.42759 / 6.25 ( 1287) metal coordination : bond 0.13506 / 7.51 ( 6) *********************** 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 : 0.414 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: 0.8250 (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: 0.0964 time to fit residues: 28.2188 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 : 0.386 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.141239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.099522 restraints weight = 21082.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.102196 restraints weight = 12377.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.103958 restraints weight = 9177.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.104870 restraints weight = 7745.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.105669 restraints weight = 7037.110| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12279 Z= 0.153 Angle : 0.710 8.281 16996 Z= 0.334 Chirality : 0.050 0.332 2052 Planarity : 0.004 0.049 1837 Dihedral : 17.080 92.555 2475 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.61 % Allowed : 14.18 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.21 (0.22), residues: 1292 helix: -1.15 (0.21), residues: 528 sheet: -3.36 (0.29), residues: 240 loop : -2.38 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 769 TYR 0.024 0.001 TYR A 650 PHE 0.025 0.001 PHE B 324 TRP 0.010 0.001 TRP A 452 HIS 0.006 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (12268) covalent geometry : angle 0.70925 / 0.33 (16986) SS BOND : bond 0.00296 / 0.15 ( 5) SS BOND : angle 1.56112 / 0.67 ( 10) hydrogen bonds : bond 0.05727 / 4.07 ( 487) hydrogen bonds : angle 5.16557 / 3.51 ( 1287) metal coordination : bond 0.00579 / 0.30 ( 6) *********************** 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 202 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7497 (pm20) REVERT: B 322 MET cc_start: 0.8148 (mmt) cc_final: 0.7932 (mmt) REVERT: B 484 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8899 (tp) REVERT: B 563 MET cc_start: 0.7261 (mtt) cc_final: 0.6149 (tmm) REVERT: B 676 TYR cc_start: 0.7820 (t80) cc_final: 0.7611 (t80) REVERT: A 193 LYS cc_start: 0.9200 (tptt) cc_final: 0.8880 (tttp) REVERT: A 219 TYR cc_start: 0.8066 (m-80) cc_final: 0.7593 (m-10) REVERT: A 261 ILE cc_start: 0.9164 (mt) cc_final: 0.8923 (mm) REVERT: A 323 ILE cc_start: 0.9149 (pt) cc_final: 0.8944 (mt) REVERT: A 637 MET cc_start: 0.7318 (ttp) cc_final: 0.6114 (tmm) REVERT: A 641 MET cc_start: 0.5257 (ptt) cc_final: 0.4837 (ptt) REVERT: A 672 MET cc_start: 0.8955 (mtm) cc_final: 0.8070 (tpt) REVERT: A 681 LYS cc_start: 0.9028 (tttp) cc_final: 0.8116 (tttt) REVERT: A 728 ASN cc_start: 0.8069 (p0) cc_final: 0.7495 (p0) REVERT: A 741 ASP cc_start: 0.8196 (m-30) cc_final: 0.7746 (m-30) outliers start: 18 outliers final: 10 residues processed: 193 average time/residue: 0.0800 time to fit residues: 23.7255 Evaluate side-chains 154 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 619 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 Chi-restraints excluded: chain A residue 733 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 17 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 106 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 486 ASN ** 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 129 GLN A 148 ASN ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.134932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.093688 restraints weight = 21624.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.096197 restraints weight = 12683.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.097776 restraints weight = 9419.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.098531 restraints weight = 7965.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.099290 restraints weight = 7289.192| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 12279 Z= 0.327 Angle : 0.814 10.937 16996 Z= 0.388 Chirality : 0.052 0.222 2052 Planarity : 0.004 0.048 1837 Dihedral : 17.013 101.944 2475 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 4.19 % Allowed : 16.50 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.23), residues: 1292 helix: -0.87 (0.22), residues: 547 sheet: -3.21 (0.29), residues: 243 loop : -2.33 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 504 TYR 0.022 0.002 TYR A 650 PHE 0.031 0.002 PHE A 131 TRP 0.023 0.002 TRP A 452 HIS 0.007 0.002 HIS A 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00752 / 0.33 (12268) covalent geometry : angle 0.81206 / 0.39 (16986) SS BOND : bond 0.00520 / 0.33 ( 5) SS BOND : angle 2.34205 / 1.29 ( 10) hydrogen bonds : bond 0.05845 / 4.08 ( 487) hydrogen bonds : angle 5.09235 / 3.43 ( 1287) metal coordination : bond 0.00999 / 0.58 ( 6) *********************** 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 201 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 154 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 484 ILE cc_start: 0.9126 (tp) cc_final: 0.8666 (tp) REVERT: B 563 MET cc_start: 0.7621 (mtt) cc_final: 0.6308 (tmm) REVERT: A 106 LYS cc_start: 0.8703 (mttt) cc_final: 0.8426 (mttm) REVERT: A 219 TYR cc_start: 0.8340 (m-80) cc_final: 0.8011 (m-10) REVERT: A 299 LYS cc_start: 0.8294 (mtpp) cc_final: 0.8058 (mttt) REVERT: A 323 ILE cc_start: 0.9164 (pt) cc_final: 0.8925 (mt) REVERT: A 522 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.8240 (t70) REVERT: A 681 LYS cc_start: 0.8949 (tttp) cc_final: 0.8674 (tttt) REVERT: A 728 ASN cc_start: 0.8160 (p0) cc_final: 0.7546 (p0) REVERT: A 741 ASP cc_start: 0.8051 (m-30) cc_final: 0.7701 (m-30) outliers start: 47 outliers final: 31 residues processed: 188 average time/residue: 0.0733 time to fit residues: 21.9736 Evaluate side-chains 173 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 62 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 264 THR 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 652 THR 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 Chi-restraints excluded: chain A residue 749 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 166 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 129 GLN A 148 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.135743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.094329 restraints weight = 21549.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.096854 restraints weight = 12748.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.098534 restraints weight = 9476.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.099571 restraints weight = 7971.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.100046 restraints weight = 7202.779| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 12279 Z= 0.274 Angle : 0.754 9.159 16996 Z= 0.360 Chirality : 0.050 0.217 2052 Planarity : 0.004 0.050 1837 Dihedral : 16.908 109.579 2475 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 4.82 % Allowed : 19.36 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.23), residues: 1292 helix: -0.54 (0.22), residues: 541 sheet: -3.06 (0.30), residues: 243 loop : -2.11 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 504 TYR 0.023 0.002 TYR A 650 PHE 0.029 0.002 PHE A 131 TRP 0.019 0.002 TRP B 452 HIS 0.005 0.001 HIS A 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.27 (12268) covalent geometry : angle 0.75316 / 0.36 (16986) SS BOND : bond 0.00455 / 0.27 ( 5) SS BOND : angle 1.94605 / 0.98 ( 10) hydrogen bonds : bond 0.05284 / 3.73 ( 487) hydrogen bonds : angle 4.86427 / 3.28 ( 1287) metal coordination : bond 0.00791 / 0.45 ( 6) *********************** 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 199 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 145 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 484 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8903 (tp) REVERT: A 106 LYS cc_start: 0.8650 (mttt) cc_final: 0.8402 (mttm) REVERT: A 219 TYR cc_start: 0.8219 (m-80) cc_final: 0.7866 (m-10) REVERT: A 314 TYR cc_start: 0.8524 (m-80) cc_final: 0.8155 (m-80) REVERT: A 450 HIS cc_start: 0.7790 (OUTLIER) cc_final: 0.7243 (t70) REVERT: A 452 TRP cc_start: 0.9075 (OUTLIER) cc_final: 0.8734 (t-100) REVERT: A 522 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.8249 (t70) REVERT: A 637 MET cc_start: 0.7448 (tmm) cc_final: 0.6921 (ptt) REVERT: A 672 MET cc_start: 0.8846 (mtp) cc_final: 0.8024 (tpt) REVERT: A 681 LYS cc_start: 0.8941 (tttp) cc_final: 0.8665 (tttt) REVERT: A 728 ASN cc_start: 0.8186 (p0) cc_final: 0.7615 (p0) outliers start: 54 outliers final: 35 residues processed: 183 average time/residue: 0.0729 time to fit residues: 21.0026 Evaluate side-chains 177 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 138 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 90 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 555 ILE 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 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 195 THR 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 450 HIS Chi-restraints excluded: chain A residue 452 TRP 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 599 THR 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 641 MET Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 749 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 52 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 ASN A 129 GLN A 166 HIS A 174 GLN A 466 HIS ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.138472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.097583 restraints weight = 21122.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.100198 restraints weight = 12604.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.101881 restraints weight = 9344.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.102940 restraints weight = 7844.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.103283 restraints weight = 7086.867| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12279 Z= 0.154 Angle : 0.662 9.315 16996 Z= 0.311 Chirality : 0.047 0.213 2052 Planarity : 0.003 0.046 1837 Dihedral : 16.644 113.754 2475 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.37 % Allowed : 20.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.24), residues: 1292 helix: -0.23 (0.23), residues: 543 sheet: -2.78 (0.31), residues: 244 loop : -1.92 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 478 TYR 0.023 0.001 TYR A 650 PHE 0.020 0.001 PHE A 131 TRP 0.012 0.001 TRP A 452 HIS 0.005 0.001 HIS B 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (12268) covalent geometry : angle 0.66103 / 0.31 (16986) SS BOND : bond 0.00324 / 0.17 ( 5) SS BOND : angle 1.46878 / 0.66 ( 10) hydrogen bonds : bond 0.04667 / 3.27 ( 487) hydrogen bonds : angle 4.60390 / 3.11 ( 1287) metal coordination : bond 0.00351 / 0.20 ( 6) *********************** 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 202 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 153 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 260 ASP cc_start: 0.8711 (m-30) cc_final: 0.8499 (m-30) REVERT: B 563 MET cc_start: 0.7351 (mtm) cc_final: 0.6063 (tmm) REVERT: A 44 MET cc_start: 0.7549 (ppp) cc_final: 0.7096 (ppp) REVERT: A 88 ASP cc_start: 0.7476 (p0) cc_final: 0.6954 (p0) REVERT: A 219 TYR cc_start: 0.8186 (m-80) cc_final: 0.7810 (m-80) REVERT: A 299 LYS cc_start: 0.8189 (mttt) cc_final: 0.7946 (mttt) REVERT: A 314 TYR cc_start: 0.8487 (m-80) cc_final: 0.8186 (m-80) REVERT: A 450 HIS cc_start: 0.7753 (OUTLIER) cc_final: 0.7249 (t70) REVERT: A 522 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.8212 (t0) REVERT: A 637 MET cc_start: 0.7576 (tmm) cc_final: 0.7013 (ptt) REVERT: A 666 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.8122 (m-10) REVERT: A 728 ASN cc_start: 0.8106 (p0) cc_final: 0.7493 (p0) outliers start: 49 outliers final: 29 residues processed: 190 average time/residue: 0.0696 time to fit residues: 21.2879 Evaluate side-chains 176 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 168 THR Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 463 MET 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 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 211 ILE 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 579 THR 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 666 PHE 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 Chi-restraints excluded: chain A residue 749 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 105 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 108 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.138682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.097696 restraints weight = 21109.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.100308 restraints weight = 12644.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.101577 restraints weight = 9424.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.102903 restraints weight = 8091.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.103485 restraints weight = 7261.152| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12279 Z= 0.153 Angle : 0.651 9.975 16996 Z= 0.305 Chirality : 0.046 0.206 2052 Planarity : 0.003 0.046 1837 Dihedral : 16.457 120.060 2473 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.10 % Allowed : 21.50 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.24), residues: 1292 helix: -0.03 (0.23), residues: 543 sheet: -2.63 (0.31), residues: 248 loop : -1.74 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 478 TYR 0.023 0.001 TYR A 650 PHE 0.023 0.001 PHE B 591 TRP 0.013 0.001 TRP A 452 HIS 0.005 0.001 HIS B 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (12268) covalent geometry : angle 0.65005 / 0.31 (16986) SS BOND : bond 0.00306 / 0.16 ( 5) SS BOND : angle 1.39107 / 0.63 ( 10) hydrogen bonds : bond 0.04484 / 3.14 ( 487) hydrogen bonds : angle 4.46247 / 3.02 ( 1287) metal coordination : bond 0.00363 / 0.21 ( 6) *********************** 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 199 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 153 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 260 ASP cc_start: 0.8767 (m-30) cc_final: 0.8522 (m-30) REVERT: B 676 TYR cc_start: 0.7478 (OUTLIER) cc_final: 0.6574 (t80) REVERT: B 680 MET cc_start: 0.8107 (mtp) cc_final: 0.7759 (mtp) REVERT: A 69 LEU cc_start: 0.9309 (mt) cc_final: 0.9091 (mt) REVERT: A 88 ASP cc_start: 0.7521 (p0) cc_final: 0.6987 (p0) REVERT: A 219 TYR cc_start: 0.8188 (m-80) cc_final: 0.7900 (m-80) REVERT: A 299 LYS cc_start: 0.8205 (mttt) cc_final: 0.7933 (mttt) REVERT: A 314 TYR cc_start: 0.8426 (m-80) cc_final: 0.8174 (m-80) REVERT: A 450 HIS cc_start: 0.7773 (OUTLIER) cc_final: 0.7254 (t70) REVERT: A 637 MET cc_start: 0.7558 (tmm) cc_final: 0.6901 (ptt) REVERT: A 675 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.7035 (mmp) REVERT: A 728 ASN cc_start: 0.8067 (p0) cc_final: 0.7474 (p0) outliers start: 46 outliers final: 35 residues processed: 186 average time/residue: 0.0757 time to fit residues: 22.5828 Evaluate side-chains 178 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 555 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 676 TYR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 211 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 579 THR 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 641 MET Chi-restraints excluded: chain A residue 675 MET 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 Chi-restraints excluded: chain A residue 749 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 35 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 41 optimal weight: 0.6980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.139884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.098452 restraints weight = 20877.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.101126 restraints weight = 12215.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.102850 restraints weight = 9052.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.103936 restraints weight = 7606.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.104433 restraints weight = 6866.720| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12279 Z= 0.195 Angle : 0.676 9.789 16996 Z= 0.319 Chirality : 0.047 0.205 2052 Planarity : 0.003 0.045 1837 Dihedral : 16.494 127.918 2473 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.91 % Allowed : 20.87 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.24), residues: 1292 helix: -0.01 (0.23), residues: 543 sheet: -2.60 (0.31), residues: 248 loop : -1.69 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 504 TYR 0.022 0.001 TYR A 650 PHE 0.029 0.001 PHE A 296 TRP 0.014 0.001 TRP A 452 HIS 0.005 0.001 HIS B 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (12268) covalent geometry : angle 0.67559 / 0.32 (16986) SS BOND : bond 0.00388 / 0.21 ( 5) SS BOND : angle 1.54401 / 0.73 ( 10) hydrogen bonds : bond 0.04555 / 3.21 ( 487) hydrogen bonds : angle 4.49981 / 3.04 ( 1287) metal coordination : bond 0.00747 / 0.38 ( 6) *********************** 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 202 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 147 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 260 ASP cc_start: 0.8819 (m-30) cc_final: 0.8591 (m-30) REVERT: B 676 TYR cc_start: 0.7532 (OUTLIER) cc_final: 0.6436 (t80) REVERT: B 680 MET cc_start: 0.8024 (mtp) cc_final: 0.7598 (mtt) REVERT: A 69 LEU cc_start: 0.9310 (mt) cc_final: 0.9095 (mt) REVERT: A 88 ASP cc_start: 0.7448 (p0) cc_final: 0.6912 (p0) REVERT: A 219 TYR cc_start: 0.8088 (m-80) cc_final: 0.7795 (m-80) REVERT: A 299 LYS cc_start: 0.8229 (mttt) cc_final: 0.8000 (mttt) REVERT: A 314 TYR cc_start: 0.8463 (m-80) cc_final: 0.8200 (m-80) REVERT: A 450 HIS cc_start: 0.7766 (OUTLIER) cc_final: 0.7230 (t70) REVERT: A 452 TRP cc_start: 0.9065 (OUTLIER) cc_final: 0.8766 (t-100) REVERT: A 637 MET cc_start: 0.7544 (tmm) cc_final: 0.6900 (ptt) REVERT: A 666 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.8364 (m-80) REVERT: A 675 MET cc_start: 0.7357 (OUTLIER) cc_final: 0.6994 (mmp) REVERT: A 728 ASN cc_start: 0.8068 (p0) cc_final: 0.7441 (p0) outliers start: 55 outliers final: 44 residues processed: 188 average time/residue: 0.0732 time to fit residues: 22.0199 Evaluate side-chains 189 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 140 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 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 322 MET Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 PHE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 676 TYR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 81 SER 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 194 LEU 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 449 PHE Chi-restraints excluded: chain A residue 450 HIS Chi-restraints excluded: chain A residue 452 TRP 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 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 641 MET Chi-restraints excluded: chain A residue 666 PHE Chi-restraints excluded: chain A residue 675 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 Chi-restraints excluded: chain A residue 749 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 10 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 64 optimal weight: 0.4980 chunk 53 optimal weight: 0.2980 chunk 132 optimal weight: 20.0000 chunk 108 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.142081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.100999 restraints weight = 20831.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.103855 restraints weight = 11928.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.105708 restraints weight = 8701.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.106812 restraints weight = 7247.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.107191 restraints weight = 6516.442| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12279 Z= 0.135 Angle : 0.645 12.048 16996 Z= 0.302 Chirality : 0.046 0.209 2052 Planarity : 0.003 0.046 1837 Dihedral : 16.389 138.581 2473 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.66 % Allowed : 22.39 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.24), residues: 1292 helix: 0.13 (0.23), residues: 542 sheet: -2.35 (0.32), residues: 238 loop : -1.54 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 504 TYR 0.023 0.001 TYR A 650 PHE 0.027 0.001 PHE A 296 TRP 0.011 0.001 TRP A 452 HIS 0.005 0.001 HIS B 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (12268) covalent geometry : angle 0.64475 / 0.30 (16986) SS BOND : bond 0.00206 / 0.11 ( 5) SS BOND : angle 1.18517 / 0.51 ( 10) hydrogen bonds : bond 0.04364 / 3.08 ( 487) hydrogen bonds : angle 4.38064 / 2.96 ( 1287) metal coordination : bond 0.00553 / 0.29 ( 6) *********************** 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 201 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 676 TYR cc_start: 0.7491 (OUTLIER) cc_final: 0.6372 (t80) REVERT: B 680 MET cc_start: 0.8015 (mtp) cc_final: 0.7575 (mtt) REVERT: A 88 ASP cc_start: 0.7465 (p0) cc_final: 0.6901 (p0) REVERT: A 219 TYR cc_start: 0.7960 (m-80) cc_final: 0.7692 (m-80) REVERT: A 450 HIS cc_start: 0.7771 (OUTLIER) cc_final: 0.7222 (t70) REVERT: A 452 TRP cc_start: 0.9044 (OUTLIER) cc_final: 0.8717 (t-100) REVERT: A 520 LEU cc_start: 0.8222 (mm) cc_final: 0.7867 (mt) REVERT: A 533 SER cc_start: 0.8797 (t) cc_final: 0.8487 (t) REVERT: A 637 MET cc_start: 0.7522 (tmm) cc_final: 0.6859 (ptt) REVERT: A 666 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.8204 (m-80) REVERT: A 675 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.7013 (mmp) REVERT: A 728 ASN cc_start: 0.8056 (p0) cc_final: 0.7485 (p0) outliers start: 41 outliers final: 32 residues processed: 193 average time/residue: 0.0718 time to fit residues: 22.2462 Evaluate side-chains 183 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 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 439 LEU Chi-restraints excluded: chain B residue 449 PHE Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 676 TYR Chi-restraints excluded: chain B residue 700 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 194 LEU 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 452 TRP 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 599 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 666 PHE Chi-restraints excluded: chain A residue 675 MET 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 749 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 4 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 114 optimal weight: 0.6980 chunk 126 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN 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 = 0.140131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.098736 restraints weight = 20687.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.101432 restraints weight = 12172.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.103139 restraints weight = 9033.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.104042 restraints weight = 7606.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.104803 restraints weight = 6916.044| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12279 Z= 0.198 Angle : 0.686 10.358 16996 Z= 0.325 Chirality : 0.047 0.210 2052 Planarity : 0.003 0.044 1837 Dihedral : 16.471 151.148 2473 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 4.55 % Allowed : 21.59 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.24), residues: 1292 helix: 0.13 (0.23), residues: 543 sheet: -2.34 (0.32), residues: 249 loop : -1.44 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 60 TYR 0.022 0.002 TYR A 650 PHE 0.030 0.002 PHE A 296 TRP 0.015 0.001 TRP A 452 HIS 0.005 0.001 HIS B 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (12268) covalent geometry : angle 0.68479 / 0.32 (16986) SS BOND : bond 0.00388 / 0.23 ( 5) SS BOND : angle 1.54757 / 0.77 ( 10) hydrogen bonds : bond 0.04551 / 3.21 ( 487) hydrogen bonds : angle 4.50212 / 3.04 ( 1287) metal coordination : bond 0.01291 / 0.66 ( 6) *********************** 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: 51 poor density : 148 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 676 TYR cc_start: 0.7641 (OUTLIER) cc_final: 0.6608 (t80) REVERT: B 680 MET cc_start: 0.8071 (mtp) cc_final: 0.7663 (mtp) REVERT: A 88 ASP cc_start: 0.7494 (p0) cc_final: 0.6947 (p0) REVERT: A 219 TYR cc_start: 0.8041 (m-80) cc_final: 0.7719 (m-80) REVERT: A 314 TYR cc_start: 0.8401 (m-80) cc_final: 0.8118 (m-80) REVERT: A 450 HIS cc_start: 0.7763 (OUTLIER) cc_final: 0.7229 (t70) REVERT: A 452 TRP cc_start: 0.9068 (OUTLIER) cc_final: 0.8766 (t-100) REVERT: A 522 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.8111 (t0) REVERT: A 637 MET cc_start: 0.7559 (tmm) cc_final: 0.6190 (tmm) REVERT: A 666 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.8398 (m-80) REVERT: A 675 MET cc_start: 0.7380 (OUTLIER) cc_final: 0.7037 (mmp) REVERT: A 728 ASN cc_start: 0.8090 (p0) cc_final: 0.7448 (p0) outliers start: 51 outliers final: 42 residues processed: 184 average time/residue: 0.0732 time to fit residues: 21.5952 Evaluate side-chains 190 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 142 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 322 MET Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 PHE Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 676 TYR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 81 SER 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 194 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 449 PHE Chi-restraints excluded: chain A residue 450 HIS Chi-restraints excluded: chain A residue 452 TRP 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 599 THR 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 641 MET Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 666 PHE Chi-restraints excluded: chain A residue 675 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 749 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 131 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 158 ASN ** B 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.141508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.100544 restraints weight = 21009.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.103177 restraints weight = 13116.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.105012 restraints weight = 8889.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.105175 restraints weight = 7585.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.105580 restraints weight = 7494.161| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12279 Z= 0.147 Angle : 0.652 12.116 16996 Z= 0.304 Chirality : 0.046 0.213 2052 Planarity : 0.003 0.047 1837 Dihedral : 16.426 158.417 2473 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.19 % Allowed : 22.48 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.24), residues: 1292 helix: 0.28 (0.23), residues: 538 sheet: -2.06 (0.34), residues: 240 loop : -1.42 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 504 TYR 0.023 0.001 TYR A 650 PHE 0.032 0.001 PHE A 755 TRP 0.012 0.001 TRP A 452 HIS 0.006 0.001 HIS B 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (12268) covalent geometry : angle 0.65109 / 0.30 (16986) SS BOND : bond 0.00263 / 0.13 ( 5) SS BOND : angle 1.22176 / 0.54 ( 10) hydrogen bonds : bond 0.04418 / 3.10 ( 487) hydrogen bonds : angle 4.39042 / 2.97 ( 1287) metal coordination : bond 0.00938 / 0.49 ( 6) ********************** 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 205 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 158 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 LEU cc_start: 0.8974 (mt) cc_final: 0.8602 (tt) REVERT: B 676 TYR cc_start: 0.7541 (OUTLIER) cc_final: 0.6712 (t80) REVERT: A 88 ASP cc_start: 0.7540 (p0) cc_final: 0.7235 (p0) REVERT: A 219 TYR cc_start: 0.7991 (m-80) cc_final: 0.7725 (m-80) REVERT: A 314 TYR cc_start: 0.8377 (m-80) cc_final: 0.8106 (m-80) REVERT: A 450 HIS cc_start: 0.7788 (OUTLIER) cc_final: 0.7244 (t70) REVERT: A 452 TRP cc_start: 0.9061 (OUTLIER) cc_final: 0.8735 (t-100) REVERT: A 484 ILE cc_start: 0.8933 (tp) cc_final: 0.8551 (tp) REVERT: A 522 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.8079 (t0) REVERT: A 637 MET cc_start: 0.7554 (tmm) cc_final: 0.6877 (ptt) REVERT: A 666 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.8207 (m-80) REVERT: A 675 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.7151 (mmp) REVERT: A 728 ASN cc_start: 0.8017 (p0) cc_final: 0.7414 (p0) outliers start: 47 outliers final: 38 residues processed: 195 average time/residue: 0.0721 time to fit residues: 22.9498 Evaluate side-chains 192 residues out of total 1171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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 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 439 LEU Chi-restraints excluded: chain B residue 449 PHE Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 676 TYR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 449 PHE Chi-restraints excluded: chain A residue 450 HIS Chi-restraints excluded: chain A residue 452 TRP 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 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 641 MET Chi-restraints excluded: chain A residue 666 PHE Chi-restraints excluded: chain A residue 675 MET 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 749 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 47 optimal weight: 0.0470 chunk 23 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 75 optimal weight: 0.0770 chunk 72 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.141590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.101075 restraints weight = 20693.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.104061 restraints weight = 12963.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.105567 restraints weight = 8569.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.105635 restraints weight = 7439.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.105956 restraints weight = 7407.949| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.132 12279 Z= 0.174 Angle : 0.906 59.199 16996 Z= 0.486 Chirality : 0.048 0.605 2052 Planarity : 0.003 0.045 1837 Dihedral : 16.439 158.410 2473 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.19 % Allowed : 22.93 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.24), residues: 1292 helix: 0.30 (0.23), residues: 538 sheet: -2.06 (0.33), residues: 240 loop : -1.41 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 504 TYR 0.023 0.001 TYR A 650 PHE 0.032 0.001 PHE A 755 TRP 0.011 0.001 TRP A 452 HIS 0.005 0.001 HIS B 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (12268) covalent geometry : angle 0.90623 / 0.49 (16986) SS BOND : bond 0.00268 / 0.14 ( 5) SS BOND : angle 1.20076 / 0.52 ( 10) hydrogen bonds : bond 0.04476 / 3.11 ( 487) hydrogen bonds : angle 4.45700 / 3.03 ( 1287) metal coordination : bond 0.00825 / 0.42 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1718.88 seconds wall clock time: 30 minutes 38.46 seconds (1838.46 seconds total)