Starting phenix.real_space_refine on Mon Jul 28 02:29:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6p48_20246/07_2025/6p48_20246.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p48_20246/07_2025/6p48_20246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6p48_20246/07_2025/6p48_20246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p48_20246/07_2025/6p48_20246.map" model { file = "/net/cci-nas-00/data/ceres_data/6p48_20246/07_2025/6p48_20246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p48_20246/07_2025/6p48_20246.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 68 5.16 5 C 6592 2.51 5 N 1586 2.21 5 O 1688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9936 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4967 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 577} Chain breaks: 9 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 9.42, per 1000 atoms: 0.95 Number of scatterers: 9936 At special positions: 0 Unit cell: (85.779, 112.254, 109.077, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 68 16.00 O 1688 8.00 N 1586 7.00 C 6592 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 356 " distance=2.04 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 356 " distance=2.04 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 1.2 seconds 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2296 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 2 sheets defined 60.1% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 91 through 104 removed outlier: 3.994A pdb=" N LYS A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N TYR A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU A 102 " --> pdb=" O ARG A 98 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A 103 " --> pdb=" O GLN A 99 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASN A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 220 removed outlier: 3.787A pdb=" N ARG A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG A 219 " --> pdb=" O PHE A 215 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.626A pdb=" N VAL A 237 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A 238 " --> pdb=" O ASN A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 272 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.685A pdb=" N TRP A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN A 308 " --> pdb=" O GLY A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 326 removed outlier: 3.834A pdb=" N VAL A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N CYS A 320 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR A 325 " --> pdb=" O PHE A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 376 removed outlier: 3.837A pdb=" N SER A 376 " --> pdb=" O CYS A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 408 removed outlier: 3.856A pdb=" N GLU A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 456 removed outlier: 3.558A pdb=" N CYS A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 452 through 456' Processing helix chain 'A' and resid 456 through 480 removed outlier: 3.729A pdb=" N PHE A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 465 " --> pdb=" O PHE A 461 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE A 475 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A 477 " --> pdb=" O GLY A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 486 removed outlier: 3.648A pdb=" N VAL A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 537 removed outlier: 3.818A pdb=" N PHE A 518 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A 532 " --> pdb=" O TYR A 528 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A 535 " --> pdb=" O VAL A 531 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.906A pdb=" N TYR A 547 " --> pdb=" O THR A 543 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ASN A 549 " --> pdb=" O THR A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 573 removed outlier: 4.589A pdb=" N LEU A 557 " --> pdb=" O MET A 553 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR A 569 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE A 572 " --> pdb=" O PHE A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 589 removed outlier: 3.583A pdb=" N LEU A 588 " --> pdb=" O VAL A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 614 removed outlier: 3.535A pdb=" N LEU A 605 " --> pdb=" O CYS A 601 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN A 608 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 620 Processing helix chain 'A' and resid 638 through 646 removed outlier: 3.555A pdb=" N GLY A 642 " --> pdb=" O LYS A 638 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A 644 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 654 removed outlier: 3.543A pdb=" N ASP A 653 " --> pdb=" O ARG A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 679 removed outlier: 3.765A pdb=" N GLU A 670 " --> pdb=" O TYR A 666 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET A 671 " --> pdb=" O GLU A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 709 removed outlier: 3.597A pdb=" N ASN A 696 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE A 700 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 704 " --> pdb=" O ILE A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 747 removed outlier: 3.518A pdb=" N ALA A 741 " --> pdb=" O VAL A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 760 removed outlier: 3.603A pdb=" N TYR A 756 " --> pdb=" O PRO A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 857 removed outlier: 3.511A pdb=" N SER A 848 " --> pdb=" O HIS A 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 104 removed outlier: 3.995A pdb=" N LYS B 97 " --> pdb=" O LYS B 93 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N TYR B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU B 102 " --> pdb=" O ARG B 98 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER B 103 " --> pdb=" O GLN B 99 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASN B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 220 removed outlier: 3.787A pdb=" N ARG B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL B 213 " --> pdb=" O ARG B 209 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG B 219 " --> pdb=" O PHE B 215 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 239 removed outlier: 3.626A pdb=" N VAL B 237 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER B 238 " --> pdb=" O ASN B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 272 Processing helix chain 'B' and resid 285 through 290 Processing helix chain 'B' and resid 296 through 310 removed outlier: 3.685A pdb=" N TRP B 302 " --> pdb=" O ILE B 298 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN B 308 " --> pdb=" O GLY B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 326 removed outlier: 3.834A pdb=" N VAL B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N CYS B 320 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR B 325 " --> pdb=" O PHE B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 376 removed outlier: 3.837A pdb=" N SER B 376 " --> pdb=" O CYS B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 408 removed outlier: 3.856A pdb=" N GLU B 395 " --> pdb=" O THR B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 456 removed outlier: 3.557A pdb=" N CYS B 456 " --> pdb=" O ARG B 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 452 through 456' Processing helix chain 'B' and resid 456 through 480 removed outlier: 3.728A pdb=" N PHE B 462 " --> pdb=" O SER B 458 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU B 465 " --> pdb=" O PHE B 461 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA B 469 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER B 470 " --> pdb=" O LEU B 466 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE B 475 " --> pdb=" O VAL B 471 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR B 477 " --> pdb=" O GLY B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 486 removed outlier: 3.648A pdb=" N VAL B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 537 removed outlier: 3.818A pdb=" N PHE B 518 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA B 532 " --> pdb=" O TYR B 528 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE B 535 " --> pdb=" O VAL B 531 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 551 removed outlier: 3.906A pdb=" N TYR B 547 " --> pdb=" O THR B 543 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ASN B 549 " --> pdb=" O THR B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 573 removed outlier: 4.590A pdb=" N LEU B 557 " --> pdb=" O MET B 553 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR B 569 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE B 572 " --> pdb=" O PHE B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 589 removed outlier: 3.583A pdb=" N LEU B 588 " --> pdb=" O VAL B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 614 removed outlier: 3.535A pdb=" N LEU B 605 " --> pdb=" O CYS B 601 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN B 608 " --> pdb=" O GLU B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 620 Processing helix chain 'B' and resid 638 through 646 removed outlier: 3.555A pdb=" N GLY B 642 " --> pdb=" O LYS B 638 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 644 " --> pdb=" O VAL B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 654 removed outlier: 3.542A pdb=" N ASP B 653 " --> pdb=" O ARG B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 679 removed outlier: 3.765A pdb=" N GLU B 670 " --> pdb=" O TYR B 666 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET B 671 " --> pdb=" O GLU B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 709 removed outlier: 3.597A pdb=" N ASN B 696 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE B 700 " --> pdb=" O ASN B 696 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA B 704 " --> pdb=" O ILE B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 747 removed outlier: 3.518A pdb=" N ALA B 741 " --> pdb=" O VAL B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 760 removed outlier: 3.602A pdb=" N TYR B 756 " --> pdb=" O PRO B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 857 removed outlier: 3.510A pdb=" N SER B 848 " --> pdb=" O HIS B 844 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 76 removed outlier: 3.534A pdb=" N ALA A 244 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 73 through 76 removed outlier: 3.534A pdb=" N ALA B 244 " --> pdb=" O VAL B 76 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1248 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.44 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2934 1.34 - 1.47: 2832 1.47 - 1.59: 4334 1.59 - 1.72: 0 1.72 - 1.84: 106 Bond restraints: 10206 Sorted by residual: bond pdb=" CA ALA A 571 " pdb=" C ALA A 571 " ideal model delta sigma weight residual 1.524 1.577 -0.054 1.16e-02 7.43e+03 2.15e+01 bond pdb=" CA ALA B 571 " pdb=" C ALA B 571 " ideal model delta sigma weight residual 1.524 1.577 -0.053 1.16e-02 7.43e+03 2.12e+01 bond pdb=" CA PHE A 812 " pdb=" CB PHE A 812 " ideal model delta sigma weight residual 1.526 1.464 0.063 1.53e-02 4.27e+03 1.68e+01 bond pdb=" CA PHE B 812 " pdb=" CB PHE B 812 " ideal model delta sigma weight residual 1.526 1.464 0.063 1.53e-02 4.27e+03 1.68e+01 bond pdb=" N PRO B 648 " pdb=" CD PRO B 648 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.51e+01 ... (remaining 10201 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 13089 3.04 - 6.08: 614 6.08 - 9.12: 103 9.12 - 12.16: 26 12.16 - 15.19: 12 Bond angle restraints: 13844 Sorted by residual: angle pdb=" N ARG A 478 " pdb=" CA ARG A 478 " pdb=" C ARG A 478 " ideal model delta sigma weight residual 113.88 100.31 13.57 1.23e+00 6.61e-01 1.22e+02 angle pdb=" N ARG B 478 " pdb=" CA ARG B 478 " pdb=" C ARG B 478 " ideal model delta sigma weight residual 113.88 100.33 13.55 1.23e+00 6.61e-01 1.21e+02 angle pdb=" N ALA A 274 " pdb=" CA ALA A 274 " pdb=" C ALA A 274 " ideal model delta sigma weight residual 112.68 126.47 -13.79 1.33e+00 5.65e-01 1.07e+02 angle pdb=" N ALA B 274 " pdb=" CA ALA B 274 " pdb=" C ALA B 274 " ideal model delta sigma weight residual 112.68 126.44 -13.76 1.33e+00 5.65e-01 1.07e+02 angle pdb=" N LEU B 664 " pdb=" CA LEU B 664 " pdb=" C LEU B 664 " ideal model delta sigma weight residual 112.59 100.75 11.84 1.22e+00 6.72e-01 9.42e+01 ... (remaining 13839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.48: 5026 16.48 - 32.95: 728 32.95 - 49.43: 164 49.43 - 65.90: 50 65.90 - 82.38: 8 Dihedral angle restraints: 5976 sinusoidal: 2410 harmonic: 3566 Sorted by residual: dihedral pdb=" CA ILE A 786 " pdb=" C ILE A 786 " pdb=" N THR A 787 " pdb=" CA THR A 787 " ideal model delta harmonic sigma weight residual 180.00 152.07 27.93 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA ILE B 786 " pdb=" C ILE B 786 " pdb=" N THR B 787 " pdb=" CA THR B 787 " ideal model delta harmonic sigma weight residual 180.00 152.09 27.91 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA ASP A 375 " pdb=" C ASP A 375 " pdb=" N SER A 376 " pdb=" CA SER A 376 " ideal model delta harmonic sigma weight residual -180.00 -152.43 -27.57 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 5973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1318 0.105 - 0.210: 162 0.210 - 0.315: 30 0.315 - 0.421: 24 0.421 - 0.526: 4 Chirality restraints: 1538 Sorted by residual: chirality pdb=" CA ALA B 274 " pdb=" N ALA B 274 " pdb=" C ALA B 274 " pdb=" CB ALA B 274 " both_signs ideal model delta sigma weight residual False 2.48 1.96 0.53 2.00e-01 2.50e+01 6.91e+00 chirality pdb=" CA ALA A 274 " pdb=" N ALA A 274 " pdb=" C ALA A 274 " pdb=" CB ALA A 274 " both_signs ideal model delta sigma weight residual False 2.48 1.96 0.53 2.00e-01 2.50e+01 6.90e+00 chirality pdb=" CA PRO A 340 " pdb=" N PRO A 340 " pdb=" C PRO A 340 " pdb=" CB PRO A 340 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.67e+00 ... (remaining 1535 not shown) Planarity restraints: 1686 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 541 " 0.021 2.00e-02 2.50e+03 4.27e-02 1.83e+01 pdb=" C PRO A 541 " -0.074 2.00e-02 2.50e+03 pdb=" O PRO A 541 " 0.030 2.00e-02 2.50e+03 pdb=" N ARG A 542 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 541 " 0.021 2.00e-02 2.50e+03 4.27e-02 1.82e+01 pdb=" C PRO B 541 " -0.074 2.00e-02 2.50e+03 pdb=" O PRO B 541 " 0.029 2.00e-02 2.50e+03 pdb=" N ARG B 542 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 647 " -0.069 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO A 648 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO A 648 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 648 " -0.055 5.00e-02 4.00e+02 ... (remaining 1683 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 156 2.59 - 3.17: 8430 3.17 - 3.75: 16032 3.75 - 4.32: 22064 4.32 - 4.90: 34337 Nonbonded interactions: 81019 Sorted by model distance: nonbonded pdb=" CD1 LEU A 627 " pdb=" CD PRO A 628 " model vdw 2.014 3.860 nonbonded pdb=" CD1 LEU B 627 " pdb=" CD PRO B 628 " model vdw 2.014 3.860 nonbonded pdb=" CB HIS B 275 " pdb=" CD PRO B 276 " model vdw 2.171 3.840 nonbonded pdb=" CB HIS A 275 " pdb=" CD PRO A 276 " model vdw 2.171 3.840 nonbonded pdb=" O HIS B 275 " pdb=" O SER B 278 " model vdw 2.200 3.040 ... (remaining 81014 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.290 Find NCS groups from input model: 0.180 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 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 : 0.011 0.100 10214 Z= 0.493 Angle : 1.557 15.195 13860 Z= 0.962 Chirality : 0.091 0.526 1538 Planarity : 0.011 0.103 1686 Dihedral : 16.573 82.380 3656 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 22.33 Ramachandran Plot: Outliers : 0.86 % Allowed : 6.51 % Favored : 92.64 % Rotamer: Outliers : 3.53 % Allowed : 14.68 % Favored : 81.78 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.05 (0.17), residues: 1168 helix: -4.12 (0.11), residues: 696 sheet: -3.70 (1.03), residues: 18 loop : -3.59 (0.25), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP B 463 HIS 0.008 0.002 HIS A 844 PHE 0.028 0.004 PHE B 760 TYR 0.037 0.004 TYR A 809 ARG 0.008 0.001 ARG B 209 Details of bonding type rmsd hydrogen bonds : bond 0.30919 ( 418) hydrogen bonds : angle 12.12342 ( 1248) SS BOND : bond 0.00385 ( 8) SS BOND : angle 2.24811 ( 16) covalent geometry : bond 0.01065 (10206) covalent geometry : angle 1.55569 (13844) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 200 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 HIS cc_start: 0.5230 (OUTLIER) cc_final: 0.4889 (t70) REVERT: A 298 ILE cc_start: 0.8456 (tp) cc_final: 0.8144 (tt) REVERT: A 396 PHE cc_start: 0.6698 (t80) cc_final: 0.6483 (t80) REVERT: A 403 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7517 (tm-30) REVERT: A 588 LEU cc_start: 0.6165 (OUTLIER) cc_final: 0.5903 (mm) REVERT: A 590 LYS cc_start: 0.4367 (OUTLIER) cc_final: 0.3613 (mppt) REVERT: A 671 MET cc_start: 0.8217 (mmm) cc_final: 0.7676 (mmm) REVERT: A 742 MET cc_start: 0.7116 (mmt) cc_final: 0.6810 (tpp) REVERT: A 826 ILE cc_start: 0.5232 (OUTLIER) cc_final: 0.4985 (pt) REVERT: A 853 ILE cc_start: 0.8491 (mm) cc_final: 0.8249 (mt) REVERT: B 275 HIS cc_start: 0.5514 (OUTLIER) cc_final: 0.4570 (t70) REVERT: B 298 ILE cc_start: 0.8361 (tp) cc_final: 0.8095 (tt) REVERT: B 403 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7410 (tm-30) REVERT: B 590 LYS cc_start: 0.4209 (OUTLIER) cc_final: 0.3396 (mmtt) REVERT: B 649 ARG cc_start: 0.6494 (pmt170) cc_final: 0.6141 (ptt-90) REVERT: B 750 MET cc_start: 0.5962 (mmp) cc_final: 0.5059 (ttm) outliers start: 38 outliers final: 9 residues processed: 233 average time/residue: 0.2468 time to fit residues: 78.0557 Evaluate side-chains 153 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 862 LYS Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 586 TYR Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 862 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 129 HIS A 275 HIS A 283 GLN A 620 ASN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN A 726 GLN A 740 ASN ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 ASN B 99 GLN B 129 HIS B 275 HIS B 620 ASN ** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN B 726 GLN B 740 ASN ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 825 ASN B 830 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.230398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.199724 restraints weight = 14712.358| |-----------------------------------------------------------------------------| r_work (start): 0.4457 rms_B_bonded: 3.33 r_work: 0.4239 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10214 Z= 0.197 Angle : 0.828 13.641 13860 Z= 0.444 Chirality : 0.048 0.190 1538 Planarity : 0.008 0.059 1686 Dihedral : 8.777 59.338 1361 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.02 % Favored : 92.81 % Rotamer: Outliers : 4.46 % Allowed : 16.36 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.63 (0.20), residues: 1168 helix: -2.87 (0.15), residues: 708 sheet: -3.55 (0.77), residues: 26 loop : -3.14 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 629 HIS 0.006 0.001 HIS A 275 PHE 0.022 0.002 PHE A 556 TYR 0.034 0.002 TYR A 323 ARG 0.004 0.000 ARG B 542 Details of bonding type rmsd hydrogen bonds : bond 0.07209 ( 418) hydrogen bonds : angle 7.36344 ( 1248) SS BOND : bond 0.00293 ( 8) SS BOND : angle 1.42937 ( 16) covalent geometry : bond 0.00406 (10206) covalent geometry : angle 0.82743 (13844) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 181 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 HIS cc_start: 0.6010 (OUTLIER) cc_final: 0.4782 (t-90) REVERT: A 298 ILE cc_start: 0.8213 (tp) cc_final: 0.7899 (tt) REVERT: A 403 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7655 (tm-30) REVERT: A 588 LEU cc_start: 0.6125 (OUTLIER) cc_final: 0.5851 (mm) REVERT: A 714 MET cc_start: 0.7170 (mtt) cc_final: 0.6968 (mtt) REVERT: A 826 ILE cc_start: 0.3947 (OUTLIER) cc_final: 0.3732 (pp) REVERT: B 270 TYR cc_start: 0.5317 (t80) cc_final: 0.4841 (t80) REVERT: B 275 HIS cc_start: 0.6566 (OUTLIER) cc_final: 0.4999 (t-90) REVERT: B 298 ILE cc_start: 0.8251 (tp) cc_final: 0.7950 (tt) REVERT: B 396 PHE cc_start: 0.6836 (t80) cc_final: 0.6590 (t80) REVERT: B 403 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7585 (tm-30) REVERT: B 461 PHE cc_start: 0.8274 (m-10) cc_final: 0.8042 (m-80) REVERT: B 590 LYS cc_start: 0.4772 (OUTLIER) cc_final: 0.3689 (mmtt) REVERT: B 649 ARG cc_start: 0.6795 (pmt170) cc_final: 0.6558 (ptt-90) REVERT: B 730 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7656 (mt0) outliers start: 48 outliers final: 19 residues processed: 219 average time/residue: 0.2490 time to fit residues: 78.3514 Evaluate side-chains 172 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 730 GLN Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 818 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 14 optimal weight: 0.0270 chunk 73 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 49 optimal weight: 0.2980 chunk 51 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 chunk 109 optimal weight: 1.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN B 696 ASN ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.232638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.201608 restraints weight = 15046.613| |-----------------------------------------------------------------------------| r_work (start): 0.4483 rms_B_bonded: 3.42 r_work: 0.4266 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.4266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10214 Z= 0.167 Angle : 0.722 9.447 13860 Z= 0.386 Chirality : 0.046 0.196 1538 Planarity : 0.006 0.068 1686 Dihedral : 7.535 58.969 1342 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 4.09 % Allowed : 19.61 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.22), residues: 1168 helix: -2.15 (0.17), residues: 708 sheet: -3.43 (0.77), residues: 26 loop : -2.75 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 629 HIS 0.006 0.001 HIS A 275 PHE 0.032 0.002 PHE A 461 TYR 0.039 0.002 TYR B 323 ARG 0.007 0.001 ARG A 478 Details of bonding type rmsd hydrogen bonds : bond 0.06078 ( 418) hydrogen bonds : angle 6.71465 ( 1248) SS BOND : bond 0.00144 ( 8) SS BOND : angle 1.43750 ( 16) covalent geometry : bond 0.00349 (10206) covalent geometry : angle 0.72100 (13844) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 183 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 HIS cc_start: 0.6174 (OUTLIER) cc_final: 0.5084 (t-90) REVERT: A 298 ILE cc_start: 0.7977 (tp) cc_final: 0.7621 (tt) REVERT: A 345 GLN cc_start: 0.6813 (OUTLIER) cc_final: 0.6528 (mp10) REVERT: A 403 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7545 (tm-30) REVERT: A 555 MET cc_start: 0.8123 (tpp) cc_final: 0.7892 (tpp) REVERT: A 586 TYR cc_start: 0.5253 (OUTLIER) cc_final: 0.3836 (t80) REVERT: A 588 LEU cc_start: 0.5810 (OUTLIER) cc_final: 0.5597 (mm) REVERT: A 590 LYS cc_start: 0.5177 (OUTLIER) cc_final: 0.3792 (mppt) REVERT: A 595 GLU cc_start: 0.6761 (mp0) cc_final: 0.6326 (mp0) REVERT: A 842 MET cc_start: 0.6709 (mmt) cc_final: 0.6504 (mmt) REVERT: B 275 HIS cc_start: 0.6513 (OUTLIER) cc_final: 0.5015 (t-90) REVERT: B 298 ILE cc_start: 0.8027 (tp) cc_final: 0.7690 (tt) REVERT: B 323 TYR cc_start: 0.7799 (p90) cc_final: 0.7538 (p90) REVERT: B 403 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7475 (tm-30) REVERT: B 586 TYR cc_start: 0.4950 (OUTLIER) cc_final: 0.4025 (t80) REVERT: B 590 LYS cc_start: 0.5004 (OUTLIER) cc_final: 0.3491 (mppt) REVERT: B 730 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7539 (mt0) outliers start: 44 outliers final: 26 residues processed: 216 average time/residue: 0.2000 time to fit residues: 64.1261 Evaluate side-chains 178 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 586 TYR Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 729 MET Chi-restraints excluded: chain B residue 730 GLN Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 831 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 86 optimal weight: 0.0070 chunk 96 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 99 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4831 r_free = 0.4831 target = 0.234180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.203471 restraints weight = 14834.660| |-----------------------------------------------------------------------------| r_work (start): 0.4508 rms_B_bonded: 3.45 r_work: 0.4286 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10214 Z= 0.150 Angle : 0.675 8.949 13860 Z= 0.361 Chirality : 0.045 0.163 1538 Planarity : 0.006 0.071 1686 Dihedral : 7.157 58.260 1340 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 5.02 % Allowed : 22.12 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.23), residues: 1168 helix: -1.82 (0.18), residues: 722 sheet: -3.35 (0.77), residues: 26 loop : -2.56 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 629 HIS 0.005 0.001 HIS A 275 PHE 0.027 0.002 PHE B 461 TYR 0.031 0.001 TYR B 323 ARG 0.004 0.000 ARG A 271 Details of bonding type rmsd hydrogen bonds : bond 0.05595 ( 418) hydrogen bonds : angle 6.41579 ( 1248) SS BOND : bond 0.00241 ( 8) SS BOND : angle 1.24489 ( 16) covalent geometry : bond 0.00311 (10206) covalent geometry : angle 0.67433 (13844) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 164 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 HIS cc_start: 0.6498 (OUTLIER) cc_final: 0.5075 (t-90) REVERT: A 298 ILE cc_start: 0.7976 (tp) cc_final: 0.7638 (tt) REVERT: A 377 PHE cc_start: 0.3556 (OUTLIER) cc_final: 0.2948 (t80) REVERT: A 403 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7494 (tm-30) REVERT: A 586 TYR cc_start: 0.5077 (OUTLIER) cc_final: 0.3812 (t80) REVERT: A 588 LEU cc_start: 0.5771 (OUTLIER) cc_final: 0.5531 (mm) REVERT: A 595 GLU cc_start: 0.6660 (mp0) cc_final: 0.6182 (mp0) REVERT: A 666 TYR cc_start: 0.8716 (m-10) cc_final: 0.8450 (m-80) REVERT: A 857 ILE cc_start: 0.7152 (tp) cc_final: 0.6946 (tt) REVERT: B 270 TYR cc_start: 0.5079 (t80) cc_final: 0.4865 (t80) REVERT: B 275 HIS cc_start: 0.6515 (OUTLIER) cc_final: 0.5197 (t-90) REVERT: B 298 ILE cc_start: 0.8023 (tp) cc_final: 0.7674 (tt) REVERT: B 394 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7563 (mm) REVERT: B 403 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7409 (tm-30) REVERT: B 586 TYR cc_start: 0.4926 (OUTLIER) cc_final: 0.3976 (t80) REVERT: B 730 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7538 (mt0) REVERT: B 768 HIS cc_start: 0.4600 (t-90) cc_final: 0.4341 (t-90) REVERT: B 857 ILE cc_start: 0.7078 (tp) cc_final: 0.6871 (tt) outliers start: 54 outliers final: 29 residues processed: 206 average time/residue: 0.1776 time to fit residues: 55.3369 Evaluate side-chains 186 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 586 TYR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 729 MET Chi-restraints excluded: chain B residue 730 GLN Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 831 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 68 optimal weight: 8.9990 chunk 99 optimal weight: 0.0670 chunk 103 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 82 optimal weight: 0.0170 chunk 61 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.9758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.232595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.201430 restraints weight = 14932.209| |-----------------------------------------------------------------------------| r_work (start): 0.4493 rms_B_bonded: 3.40 r_work: 0.4270 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10214 Z= 0.168 Angle : 0.693 12.485 13860 Z= 0.363 Chirality : 0.045 0.166 1538 Planarity : 0.006 0.071 1686 Dihedral : 6.911 56.302 1332 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 4.74 % Allowed : 23.23 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.23), residues: 1168 helix: -1.57 (0.18), residues: 722 sheet: -3.50 (0.74), residues: 26 loop : -2.49 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 629 HIS 0.004 0.001 HIS A 275 PHE 0.020 0.002 PHE B 461 TYR 0.046 0.001 TYR B 323 ARG 0.004 0.000 ARG A 701 Details of bonding type rmsd hydrogen bonds : bond 0.05615 ( 418) hydrogen bonds : angle 6.31079 ( 1248) SS BOND : bond 0.00152 ( 8) SS BOND : angle 1.27865 ( 16) covalent geometry : bond 0.00355 (10206) covalent geometry : angle 0.69238 (13844) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 164 time to evaluate : 1.159 Fit side-chains revert: symmetry clash REVERT: A 275 HIS cc_start: 0.6496 (OUTLIER) cc_final: 0.5255 (t-90) REVERT: A 298 ILE cc_start: 0.8010 (tp) cc_final: 0.7676 (tt) REVERT: A 377 PHE cc_start: 0.3657 (OUTLIER) cc_final: 0.3369 (t80) REVERT: A 403 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7503 (tm-30) REVERT: A 586 TYR cc_start: 0.5150 (OUTLIER) cc_final: 0.3973 (t80) REVERT: A 595 GLU cc_start: 0.6715 (mp0) cc_final: 0.6305 (mp0) REVERT: A 742 MET cc_start: 0.8159 (tpp) cc_final: 0.7803 (mmt) REVERT: A 852 PHE cc_start: 0.7603 (m-10) cc_final: 0.7391 (m-10) REVERT: A 857 ILE cc_start: 0.7109 (tp) cc_final: 0.6905 (tt) REVERT: B 138 TYR cc_start: 0.5215 (m-80) cc_final: 0.4937 (m-80) REVERT: B 275 HIS cc_start: 0.6505 (OUTLIER) cc_final: 0.5276 (t-90) REVERT: B 298 ILE cc_start: 0.8102 (tp) cc_final: 0.7755 (tt) REVERT: B 394 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7566 (mm) REVERT: B 403 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7432 (tm-30) REVERT: B 507 MET cc_start: 0.7184 (ptt) cc_final: 0.6981 (ptt) REVERT: B 586 TYR cc_start: 0.5011 (OUTLIER) cc_final: 0.4064 (t80) REVERT: B 730 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7497 (mt0) REVERT: B 742 MET cc_start: 0.7866 (tpp) cc_final: 0.7408 (mmt) REVERT: B 768 HIS cc_start: 0.4620 (t-90) cc_final: 0.4304 (t-90) outliers start: 51 outliers final: 34 residues processed: 204 average time/residue: 0.1790 time to fit residues: 54.8458 Evaluate side-chains 189 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 148 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 586 TYR Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 729 MET Chi-restraints excluded: chain B residue 730 GLN Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 818 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 78 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 1 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 283 GLN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.230762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.199204 restraints weight = 15013.715| |-----------------------------------------------------------------------------| r_work (start): 0.4473 rms_B_bonded: 3.40 r_work: 0.4250 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10214 Z= 0.183 Angle : 0.695 12.232 13860 Z= 0.365 Chirality : 0.045 0.162 1538 Planarity : 0.006 0.072 1686 Dihedral : 6.798 54.700 1330 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 5.58 % Allowed : 23.33 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.24), residues: 1168 helix: -1.41 (0.18), residues: 718 sheet: -3.61 (0.72), residues: 26 loop : -2.47 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 629 HIS 0.004 0.001 HIS A 818 PHE 0.026 0.002 PHE A 382 TYR 0.041 0.002 TYR B 323 ARG 0.004 0.000 ARG B 753 Details of bonding type rmsd hydrogen bonds : bond 0.05723 ( 418) hydrogen bonds : angle 6.27746 ( 1248) SS BOND : bond 0.00351 ( 8) SS BOND : angle 1.31070 ( 16) covalent geometry : bond 0.00392 (10206) covalent geometry : angle 0.69363 (13844) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 159 time to evaluate : 1.111 Fit side-chains revert: symmetry clash REVERT: A 101 TYR cc_start: 0.6306 (t80) cc_final: 0.6049 (t80) REVERT: A 275 HIS cc_start: 0.6517 (OUTLIER) cc_final: 0.5393 (t-90) REVERT: A 298 ILE cc_start: 0.8101 (tp) cc_final: 0.7791 (tt) REVERT: A 377 PHE cc_start: 0.3720 (OUTLIER) cc_final: 0.3419 (t80) REVERT: A 586 TYR cc_start: 0.5211 (OUTLIER) cc_final: 0.3975 (t80) REVERT: A 595 GLU cc_start: 0.6679 (mp0) cc_final: 0.6349 (mp0) REVERT: A 666 TYR cc_start: 0.8808 (m-10) cc_final: 0.8576 (m-80) REVERT: A 730 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7366 (mp10) REVERT: A 742 MET cc_start: 0.8178 (tpp) cc_final: 0.7835 (mmt) REVERT: B 138 TYR cc_start: 0.5226 (m-80) cc_final: 0.4853 (m-80) REVERT: B 275 HIS cc_start: 0.6579 (OUTLIER) cc_final: 0.5380 (t-90) REVERT: B 298 ILE cc_start: 0.8165 (tp) cc_final: 0.7827 (tt) REVERT: B 394 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7624 (mm) REVERT: B 403 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7440 (tm-30) REVERT: B 553 MET cc_start: 0.7895 (tpp) cc_final: 0.7578 (tpp) REVERT: B 565 SER cc_start: 0.7457 (OUTLIER) cc_final: 0.7202 (t) REVERT: B 586 TYR cc_start: 0.4856 (OUTLIER) cc_final: 0.3810 (t80) REVERT: B 730 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7614 (mt0) REVERT: B 742 MET cc_start: 0.8090 (tpp) cc_final: 0.7648 (mmt) REVERT: B 768 HIS cc_start: 0.4646 (t-90) cc_final: 0.4282 (t-90) outliers start: 60 outliers final: 38 residues processed: 203 average time/residue: 0.1941 time to fit residues: 59.2534 Evaluate side-chains 192 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 146 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 586 TYR Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 729 MET Chi-restraints excluded: chain B residue 730 GLN Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 818 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 23 optimal weight: 0.0060 chunk 35 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 52 optimal weight: 0.0370 chunk 107 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 overall best weight: 1.0078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 GLN A 696 ASN ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.231917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.200714 restraints weight = 15118.626| |-----------------------------------------------------------------------------| r_work (start): 0.4486 rms_B_bonded: 3.41 r_work: 0.4259 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.4259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10214 Z= 0.169 Angle : 0.694 10.714 13860 Z= 0.364 Chirality : 0.045 0.172 1538 Planarity : 0.006 0.071 1686 Dihedral : 6.710 53.132 1330 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 5.20 % Allowed : 24.44 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.24), residues: 1168 helix: -1.19 (0.18), residues: 708 sheet: -3.62 (0.73), residues: 26 loop : -2.59 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 629 HIS 0.004 0.001 HIS A 818 PHE 0.023 0.002 PHE A 382 TYR 0.039 0.001 TYR B 323 ARG 0.003 0.000 ARG A 701 Details of bonding type rmsd hydrogen bonds : bond 0.05545 ( 418) hydrogen bonds : angle 6.21593 ( 1248) SS BOND : bond 0.00401 ( 8) SS BOND : angle 1.42746 ( 16) covalent geometry : bond 0.00360 (10206) covalent geometry : angle 0.69309 (13844) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 154 time to evaluate : 1.150 Fit side-chains revert: symmetry clash REVERT: A 275 HIS cc_start: 0.6444 (OUTLIER) cc_final: 0.5615 (t-90) REVERT: A 298 ILE cc_start: 0.8025 (tp) cc_final: 0.7646 (tt) REVERT: A 377 PHE cc_start: 0.3515 (OUTLIER) cc_final: 0.3271 (t80) REVERT: A 586 TYR cc_start: 0.5193 (OUTLIER) cc_final: 0.3914 (t80) REVERT: A 595 GLU cc_start: 0.6665 (mp0) cc_final: 0.6341 (mp0) REVERT: A 730 GLN cc_start: 0.7671 (mm-40) cc_final: 0.7393 (mp10) REVERT: A 742 MET cc_start: 0.8179 (tpp) cc_final: 0.7853 (mmt) REVERT: B 138 TYR cc_start: 0.5391 (m-80) cc_final: 0.4918 (m-80) REVERT: B 275 HIS cc_start: 0.6603 (OUTLIER) cc_final: 0.5538 (t-90) REVERT: B 298 ILE cc_start: 0.8120 (tp) cc_final: 0.7764 (tt) REVERT: B 394 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7598 (mm) REVERT: B 403 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7390 (tm-30) REVERT: B 553 MET cc_start: 0.7805 (tpp) cc_final: 0.7464 (tpp) REVERT: B 565 SER cc_start: 0.7440 (OUTLIER) cc_final: 0.7192 (t) REVERT: B 586 TYR cc_start: 0.4925 (OUTLIER) cc_final: 0.3837 (t80) REVERT: B 742 MET cc_start: 0.8156 (tpp) cc_final: 0.7753 (mmt) outliers start: 56 outliers final: 37 residues processed: 198 average time/residue: 0.1866 time to fit residues: 54.9061 Evaluate side-chains 187 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 143 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 586 TYR Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 729 MET Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 818 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 103 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.231559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.200329 restraints weight = 15043.970| |-----------------------------------------------------------------------------| r_work (start): 0.4473 rms_B_bonded: 3.36 r_work: 0.4249 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10214 Z= 0.172 Angle : 0.699 10.337 13860 Z= 0.366 Chirality : 0.045 0.164 1538 Planarity : 0.006 0.071 1686 Dihedral : 6.665 53.543 1330 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 5.11 % Allowed : 25.00 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.24), residues: 1168 helix: -1.08 (0.18), residues: 710 sheet: -3.61 (0.73), residues: 26 loop : -2.55 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 629 HIS 0.004 0.001 HIS A 818 PHE 0.028 0.002 PHE B 382 TYR 0.038 0.002 TYR B 528 ARG 0.004 0.000 ARG B 478 Details of bonding type rmsd hydrogen bonds : bond 0.05526 ( 418) hydrogen bonds : angle 6.16002 ( 1248) SS BOND : bond 0.00308 ( 8) SS BOND : angle 1.39622 ( 16) covalent geometry : bond 0.00370 (10206) covalent geometry : angle 0.69783 (13844) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 145 time to evaluate : 1.071 Fit side-chains REVERT: A 275 HIS cc_start: 0.6454 (OUTLIER) cc_final: 0.5700 (t-90) REVERT: A 298 ILE cc_start: 0.8070 (tp) cc_final: 0.7704 (tt) REVERT: A 377 PHE cc_start: 0.3655 (OUTLIER) cc_final: 0.3385 (t80) REVERT: A 403 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7360 (tm-30) REVERT: A 586 TYR cc_start: 0.5125 (OUTLIER) cc_final: 0.3930 (t80) REVERT: A 595 GLU cc_start: 0.6675 (mp0) cc_final: 0.6280 (mp0) REVERT: A 730 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7350 (mp10) REVERT: A 742 MET cc_start: 0.8193 (tpp) cc_final: 0.7869 (mmt) REVERT: B 138 TYR cc_start: 0.5330 (m-80) cc_final: 0.4856 (m-80) REVERT: B 275 HIS cc_start: 0.6592 (OUTLIER) cc_final: 0.5883 (t-90) REVERT: B 298 ILE cc_start: 0.8093 (tp) cc_final: 0.7733 (tt) REVERT: B 403 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7369 (tm-30) REVERT: B 553 MET cc_start: 0.7796 (tpp) cc_final: 0.7452 (tpp) REVERT: B 565 SER cc_start: 0.7422 (OUTLIER) cc_final: 0.7176 (t) REVERT: B 586 TYR cc_start: 0.4943 (OUTLIER) cc_final: 0.3864 (t80) REVERT: B 659 MET cc_start: 0.7207 (tpp) cc_final: 0.6397 (ttp) REVERT: B 742 MET cc_start: 0.8178 (tpp) cc_final: 0.7810 (mmt) outliers start: 55 outliers final: 42 residues processed: 187 average time/residue: 0.1651 time to fit residues: 47.2970 Evaluate side-chains 183 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 135 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 586 TYR Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 729 MET Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 857 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 53 optimal weight: 0.3980 chunk 34 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 76 optimal weight: 0.0030 chunk 100 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN B 283 GLN B 544 GLN B 726 GLN ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.236115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.206089 restraints weight = 15280.104| |-----------------------------------------------------------------------------| r_work (start): 0.4537 rms_B_bonded: 3.24 r_work: 0.4308 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10214 Z= 0.154 Angle : 0.717 15.228 13860 Z= 0.369 Chirality : 0.045 0.164 1538 Planarity : 0.006 0.070 1686 Dihedral : 6.575 52.190 1330 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 4.46 % Allowed : 26.30 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.24), residues: 1168 helix: -1.01 (0.18), residues: 714 sheet: -3.43 (0.75), residues: 26 loop : -2.43 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 629 HIS 0.004 0.001 HIS A 818 PHE 0.027 0.002 PHE B 558 TYR 0.043 0.002 TYR B 528 ARG 0.003 0.000 ARG B 478 Details of bonding type rmsd hydrogen bonds : bond 0.05236 ( 418) hydrogen bonds : angle 6.02667 ( 1248) SS BOND : bond 0.00315 ( 8) SS BOND : angle 1.40332 ( 16) covalent geometry : bond 0.00330 (10206) covalent geometry : angle 0.71627 (13844) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 162 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 HIS cc_start: 0.6303 (OUTLIER) cc_final: 0.5928 (t-90) REVERT: A 298 ILE cc_start: 0.8012 (tp) cc_final: 0.7683 (tt) REVERT: A 377 PHE cc_start: 0.3448 (OUTLIER) cc_final: 0.3239 (t80) REVERT: A 403 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7195 (tm-30) REVERT: A 586 TYR cc_start: 0.5055 (OUTLIER) cc_final: 0.3933 (t80) REVERT: A 595 GLU cc_start: 0.6679 (mp0) cc_final: 0.6365 (mp0) REVERT: A 730 GLN cc_start: 0.7697 (mm-40) cc_final: 0.7428 (mp10) REVERT: A 742 MET cc_start: 0.8312 (tpp) cc_final: 0.8001 (mmt) REVERT: B 138 TYR cc_start: 0.5235 (m-80) cc_final: 0.4788 (m-80) REVERT: B 275 HIS cc_start: 0.6543 (OUTLIER) cc_final: 0.5996 (t-90) REVERT: B 298 ILE cc_start: 0.8137 (tp) cc_final: 0.7796 (tt) REVERT: B 403 GLU cc_start: 0.7507 (tm-30) cc_final: 0.7307 (tm-30) REVERT: B 565 SER cc_start: 0.7163 (OUTLIER) cc_final: 0.6744 (p) REVERT: B 586 TYR cc_start: 0.4873 (OUTLIER) cc_final: 0.3847 (t80) REVERT: B 629 TRP cc_start: 0.5628 (m-90) cc_final: 0.5306 (m-90) REVERT: B 742 MET cc_start: 0.8155 (tpp) cc_final: 0.7762 (mmt) outliers start: 48 outliers final: 38 residues processed: 197 average time/residue: 0.2029 time to fit residues: 59.3174 Evaluate side-chains 193 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 586 TYR Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 729 MET Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 857 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 55 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 726 GLN ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4831 r_free = 0.4831 target = 0.233384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.203287 restraints weight = 14951.009| |-----------------------------------------------------------------------------| r_work (start): 0.4511 rms_B_bonded: 3.22 r_work: 0.4276 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10214 Z= 0.185 Angle : 0.756 16.814 13860 Z= 0.387 Chirality : 0.046 0.203 1538 Planarity : 0.006 0.070 1686 Dihedral : 6.624 51.503 1330 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 4.74 % Allowed : 26.12 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.24), residues: 1168 helix: -0.95 (0.18), residues: 710 sheet: -3.56 (0.73), residues: 26 loop : -2.43 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 629 HIS 0.004 0.001 HIS A 818 PHE 0.026 0.002 PHE A 382 TYR 0.036 0.002 TYR B 323 ARG 0.004 0.000 ARG A 713 Details of bonding type rmsd hydrogen bonds : bond 0.05582 ( 418) hydrogen bonds : angle 6.05983 ( 1248) SS BOND : bond 0.00312 ( 8) SS BOND : angle 1.43412 ( 16) covalent geometry : bond 0.00406 (10206) covalent geometry : angle 0.75536 (13844) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 151 time to evaluate : 1.712 Fit side-chains revert: symmetry clash REVERT: A 275 HIS cc_start: 0.6342 (OUTLIER) cc_final: 0.6014 (t-90) REVERT: A 298 ILE cc_start: 0.8094 (tp) cc_final: 0.7773 (tt) REVERT: A 377 PHE cc_start: 0.3694 (OUTLIER) cc_final: 0.3480 (t80) REVERT: A 586 TYR cc_start: 0.5121 (OUTLIER) cc_final: 0.4050 (t80) REVERT: A 595 GLU cc_start: 0.6837 (mp0) cc_final: 0.6471 (mp0) REVERT: A 730 GLN cc_start: 0.7747 (mm-40) cc_final: 0.7458 (mp10) REVERT: A 742 MET cc_start: 0.8337 (tpp) cc_final: 0.8024 (mmt) REVERT: B 138 TYR cc_start: 0.5376 (m-80) cc_final: 0.4956 (m-80) REVERT: B 275 HIS cc_start: 0.6482 (OUTLIER) cc_final: 0.6043 (t-90) REVERT: B 298 ILE cc_start: 0.8161 (tp) cc_final: 0.7848 (tt) REVERT: B 565 SER cc_start: 0.7305 (OUTLIER) cc_final: 0.7102 (t) REVERT: B 573 PHE cc_start: 0.7873 (t80) cc_final: 0.7615 (t80) REVERT: B 586 TYR cc_start: 0.4740 (OUTLIER) cc_final: 0.3930 (t80) REVERT: B 629 TRP cc_start: 0.5766 (m-90) cc_final: 0.5476 (m-90) REVERT: B 730 GLN cc_start: 0.7767 (mm-40) cc_final: 0.7505 (mp10) REVERT: B 742 MET cc_start: 0.8208 (tpp) cc_final: 0.7825 (mmt) outliers start: 51 outliers final: 39 residues processed: 189 average time/residue: 0.2293 time to fit residues: 64.4505 Evaluate side-chains 187 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 142 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 586 TYR Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 729 MET Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 857 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 77 optimal weight: 0.1980 chunk 57 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 19 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 818 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 = 0.4839 r_free = 0.4839 target = 0.234556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.205601 restraints weight = 14952.207| |-----------------------------------------------------------------------------| r_work (start): 0.4557 rms_B_bonded: 3.28 r_work: 0.4309 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10214 Z= 0.163 Angle : 0.756 15.955 13860 Z= 0.387 Chirality : 0.046 0.181 1538 Planarity : 0.006 0.069 1686 Dihedral : 6.551 50.474 1330 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 4.18 % Allowed : 27.32 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.24), residues: 1168 helix: -0.90 (0.18), residues: 710 sheet: -3.49 (0.74), residues: 26 loop : -2.37 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 629 HIS 0.004 0.001 HIS A 818 PHE 0.034 0.002 PHE A 556 TYR 0.035 0.002 TYR B 323 ARG 0.003 0.000 ARG A 753 Details of bonding type rmsd hydrogen bonds : bond 0.05371 ( 418) hydrogen bonds : angle 5.99900 ( 1248) SS BOND : bond 0.00320 ( 8) SS BOND : angle 1.41076 ( 16) covalent geometry : bond 0.00355 (10206) covalent geometry : angle 0.75452 (13844) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5843.08 seconds wall clock time: 105 minutes 6.29 seconds (6306.29 seconds total)