Starting phenix.real_space_refine on Fri Feb 14 07:32:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6p48_20246/02_2025/6p48_20246.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p48_20246/02_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_20246/02_2025/6p48_20246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p48_20246/02_2025/6p48_20246.map" model { file = "/net/cci-nas-00/data/ceres_data/6p48_20246/02_2025/6p48_20246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p48_20246/02_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-5592/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: 9.39, 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=4, 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 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: 2.49 Conformation dependent library (CDL) restraints added in 1.1 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: 0.84 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: 2.63 Time building geometry restraints manager: 2.89 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: 5020 16.48 - 32.95: 724 32.95 - 49.43: 163 49.43 - 65.90: 49 65.90 - 82.38: 8 Dihedral angle restraints: 5964 sinusoidal: 2398 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 5961 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: 160 2.59 - 3.17: 8438 3.17 - 3.75: 16032 3.75 - 4.32: 22064 4.32 - 4.90: 34337 Nonbonded interactions: 81031 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=" SG CYS B 349 " pdb=" SG CYS B 807 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS B 596 " pdb=" SG CYS B 601 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS B 338 " pdb=" SG CYS B 365 " model vdw 2.031 3.760 ... (remaining 81026 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: 0.05 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: 1.040 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: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.630 Find NCS groups from input model: 0.170 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.150 ------------------------------------------------------------------------------- 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 10206 Z= 0.672 Angle : 1.556 15.195 13844 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 *********************** 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 : 1.160 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: 0.2475 time to fit residues: 78.2081 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 : 1.050 ------------------------------------------------------------------------------- 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 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 = 0.4796 r_free = 0.4796 target = 0.230592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.198802 restraints weight = 14677.967| |-----------------------------------------------------------------------------| r_work (start): 0.4451 rms_B_bonded: 3.42 r_work: 0.4226 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10206 Z= 0.255 Angle : 0.815 13.389 13844 Z= 0.436 Chirality : 0.047 0.188 1538 Planarity : 0.008 0.062 1686 Dihedral : 8.673 59.815 1361 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.85 % Favored : 92.98 % Rotamer: Outliers : 4.37 % Allowed : 16.64 % Favored : 79.00 % 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: -4.58 (0.20), residues: 1168 helix: -2.82 (0.15), residues: 708 sheet: -3.52 (0.76), residues: 26 loop : -3.12 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 629 HIS 0.005 0.001 HIS A 275 PHE 0.021 0.002 PHE A 556 TYR 0.034 0.002 TYR A 323 ARG 0.005 0.001 ARG B 542 *********************** 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 236 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 189 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 HIS cc_start: 0.5975 (OUTLIER) cc_final: 0.4775 (t-90) REVERT: A 298 ILE cc_start: 0.8197 (tp) cc_final: 0.7880 (tt) REVERT: A 403 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7652 (tm-30) REVERT: A 522 MET cc_start: 0.7290 (mmp) cc_final: 0.6982 (mmm) REVERT: A 588 LEU cc_start: 0.6082 (OUTLIER) cc_final: 0.5800 (mm) REVERT: A 826 ILE cc_start: 0.4166 (OUTLIER) cc_final: 0.3953 (pp) REVERT: B 101 TYR cc_start: 0.6255 (t80) cc_final: 0.6023 (t80) REVERT: B 270 TYR cc_start: 0.5330 (t80) cc_final: 0.4909 (t80) REVERT: B 275 HIS cc_start: 0.6553 (OUTLIER) cc_final: 0.5041 (t-90) REVERT: B 298 ILE cc_start: 0.8233 (tp) cc_final: 0.7929 (tt) REVERT: B 323 TYR cc_start: 0.7799 (p90) cc_final: 0.7580 (p90) REVERT: B 386 MET cc_start: 0.6811 (mmp) cc_final: 0.6564 (mmp) REVERT: B 403 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7588 (tm-30) REVERT: B 461 PHE cc_start: 0.8363 (m-10) cc_final: 0.8087 (m-80) REVERT: B 555 MET cc_start: 0.7934 (tpp) cc_final: 0.7718 (tpp) REVERT: B 590 LYS cc_start: 0.4803 (OUTLIER) cc_final: 0.3726 (mmtt) REVERT: B 649 ARG cc_start: 0.6851 (pmt170) cc_final: 0.6559 (ptt-90) REVERT: B 730 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7628 (mt0) REVERT: B 857 ILE cc_start: 0.7446 (tp) cc_final: 0.7211 (tt) outliers start: 47 outliers final: 20 residues processed: 226 average time/residue: 0.2081 time to fit residues: 67.3683 Evaluate side-chains 174 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 516 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: 0.8980 chunk 73 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 63 optimal weight: 0.3980 chunk 109 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 696 ASN ** 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 = 0.4811 r_free = 0.4811 target = 0.231816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.200532 restraints weight = 15014.472| |-----------------------------------------------------------------------------| r_work (start): 0.4477 rms_B_bonded: 3.42 r_work: 0.4257 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10206 Z= 0.235 Angle : 0.723 9.650 13844 Z= 0.386 Chirality : 0.046 0.177 1538 Planarity : 0.006 0.070 1686 Dihedral : 7.547 58.821 1342 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 4.37 % Allowed : 18.87 % Favored : 76.77 % 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: -2.18 (0.17), residues: 716 sheet: -3.43 (0.77), residues: 26 loop : -2.69 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 629 HIS 0.008 0.001 HIS B 275 PHE 0.031 0.002 PHE A 461 TYR 0.030 0.002 TYR A 323 ARG 0.006 0.001 ARG A 478 *********************** 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 224 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 177 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 HIS cc_start: 0.6207 (OUTLIER) cc_final: 0.5002 (t-90) REVERT: A 298 ILE cc_start: 0.8032 (tp) cc_final: 0.7688 (tt) REVERT: A 403 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7555 (tm-30) REVERT: A 555 MET cc_start: 0.8109 (tpp) cc_final: 0.7905 (tpp) REVERT: A 586 TYR cc_start: 0.5212 (OUTLIER) cc_final: 0.3823 (t80) REVERT: A 588 LEU cc_start: 0.5783 (OUTLIER) cc_final: 0.5571 (mm) REVERT: A 590 LYS cc_start: 0.5204 (OUTLIER) cc_final: 0.3831 (mppt) REVERT: A 595 GLU cc_start: 0.6710 (mp0) cc_final: 0.6242 (mp0) REVERT: B 101 TYR cc_start: 0.6287 (t80) cc_final: 0.5934 (t80) REVERT: B 275 HIS cc_start: 0.6637 (OUTLIER) cc_final: 0.5013 (t-90) REVERT: B 298 ILE cc_start: 0.8085 (tp) cc_final: 0.7744 (tt) REVERT: B 403 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7473 (tm-30) REVERT: B 586 TYR cc_start: 0.4963 (OUTLIER) cc_final: 0.4030 (t80) REVERT: B 590 LYS cc_start: 0.4988 (OUTLIER) cc_final: 0.3455 (mppt) REVERT: B 649 ARG cc_start: 0.6777 (pmt170) cc_final: 0.6521 (ptt-90) REVERT: B 666 TYR cc_start: 0.8686 (m-10) cc_final: 0.8467 (m-80) REVERT: B 730 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7557 (mt0) outliers start: 47 outliers final: 28 residues processed: 213 average time/residue: 0.1941 time to fit residues: 60.4407 Evaluate side-chains 183 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 356 CYS 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 691 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 352 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 86 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 99 optimal weight: 0.0270 chunk 34 optimal weight: 0.0570 chunk 56 optimal weight: 0.3980 chunk 19 optimal weight: 0.0170 chunk 49 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 overall best weight: 0.2394 ------------------------------------------------------------------------------- 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 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 = 0.4847 r_free = 0.4847 target = 0.236358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.206121 restraints weight = 14812.960| |-----------------------------------------------------------------------------| r_work (start): 0.4532 rms_B_bonded: 3.44 r_work: 0.4309 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.4309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6517 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10206 Z= 0.179 Angle : 0.668 9.207 13844 Z= 0.356 Chirality : 0.044 0.168 1538 Planarity : 0.006 0.071 1686 Dihedral : 7.068 58.875 1340 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 4.37 % Allowed : 21.19 % Favored : 74.44 % 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: -3.21 (0.23), residues: 1168 helix: -1.70 (0.18), residues: 714 sheet: -3.30 (0.79), residues: 26 loop : -2.60 (0.30), residues: 428 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 0.029 0.002 PHE B 461 TYR 0.026 0.001 TYR A 323 ARG 0.004 0.000 ARG A 271 *********************** 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 223 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 176 time to evaluate : 1.126 Fit side-chains REVERT: A 275 HIS cc_start: 0.6492 (OUTLIER) cc_final: 0.5196 (t-90) REVERT: A 298 ILE cc_start: 0.7912 (tp) cc_final: 0.7560 (tt) REVERT: A 403 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7537 (tm-30) REVERT: A 586 TYR cc_start: 0.5047 (OUTLIER) cc_final: 0.3838 (t80) REVERT: A 588 LEU cc_start: 0.5720 (OUTLIER) cc_final: 0.5482 (mm) REVERT: A 595 GLU cc_start: 0.6712 (mp0) cc_final: 0.6271 (mp0) REVERT: A 666 TYR cc_start: 0.8717 (m-10) cc_final: 0.8469 (m-80) REVERT: A 852 PHE cc_start: 0.7584 (m-10) cc_final: 0.7350 (m-10) REVERT: B 101 TYR cc_start: 0.6261 (t80) cc_final: 0.5967 (t80) REVERT: B 275 HIS cc_start: 0.6599 (OUTLIER) cc_final: 0.5093 (t-90) REVERT: B 298 ILE cc_start: 0.7967 (tp) cc_final: 0.7605 (tt) REVERT: B 394 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7486 (mm) REVERT: B 403 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7433 (tm-30) REVERT: B 586 TYR cc_start: 0.4841 (OUTLIER) cc_final: 0.4002 (t80) REVERT: B 730 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7499 (mt0) REVERT: B 768 HIS cc_start: 0.4545 (t-90) cc_final: 0.4312 (t-90) outliers start: 47 outliers final: 29 residues processed: 211 average time/residue: 0.1894 time to fit residues: 58.4789 Evaluate side-chains 188 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 352 CYS 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 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 220 VAL Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 352 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 68 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 82 optimal weight: 0.0870 chunk 61 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- 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 562 ASN ** 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 = 0.4818 r_free = 0.4818 target = 0.232135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.200164 restraints weight = 15001.216| |-----------------------------------------------------------------------------| r_work (start): 0.4476 rms_B_bonded: 3.47 r_work: 0.4260 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10206 Z= 0.243 Angle : 0.710 12.756 13844 Z= 0.371 Chirality : 0.045 0.169 1538 Planarity : 0.006 0.072 1686 Dihedral : 6.915 56.746 1332 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 4.74 % Allowed : 22.40 % 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: -2.96 (0.23), residues: 1168 helix: -1.51 (0.18), residues: 718 sheet: -3.47 (0.76), residues: 26 loop : -2.47 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 629 HIS 0.004 0.001 HIS A 275 PHE 0.026 0.002 PHE A 382 TYR 0.025 0.002 TYR A 323 ARG 0.007 0.000 ARG B 753 *********************** 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 209 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 158 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 275 HIS cc_start: 0.6492 (OUTLIER) cc_final: 0.5234 (t-90) REVERT: A 298 ILE cc_start: 0.8068 (tp) cc_final: 0.7731 (tt) REVERT: A 377 PHE cc_start: 0.3425 (OUTLIER) cc_final: 0.3126 (t80) REVERT: A 403 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7524 (tm-30) REVERT: A 586 TYR cc_start: 0.5154 (OUTLIER) cc_final: 0.3995 (t80) REVERT: A 595 GLU cc_start: 0.6741 (mp0) cc_final: 0.6318 (mp0) REVERT: A 742 MET cc_start: 0.8182 (tpp) cc_final: 0.7830 (mmt) REVERT: B 101 TYR cc_start: 0.6220 (t80) cc_final: 0.5893 (t80) REVERT: B 138 TYR cc_start: 0.5183 (m-80) cc_final: 0.4911 (m-80) REVERT: B 270 TYR cc_start: 0.5103 (t80) cc_final: 0.4872 (t80) REVERT: B 275 HIS cc_start: 0.6805 (OUTLIER) cc_final: 0.5962 (t-90) REVERT: B 298 ILE cc_start: 0.8139 (tp) cc_final: 0.7791 (tt) REVERT: B 394 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7554 (mm) REVERT: B 403 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7421 (tm-30) REVERT: B 586 TYR cc_start: 0.5039 (OUTLIER) cc_final: 0.4089 (t80) REVERT: B 768 HIS cc_start: 0.4623 (t-90) cc_final: 0.4304 (t-90) outliers start: 51 outliers final: 32 residues processed: 199 average time/residue: 0.1926 time to fit residues: 56.7227 Evaluate side-chains 182 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 144 time to evaluate : 1.233 ------------------------------------------------------------------------------- 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 474 ILE Chi-restraints excluded: chain A residue 504 THR 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 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 504 THR 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 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: 0.9990 chunk 58 optimal weight: 0.9980 chunk 1 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 107 optimal weight: 0.3980 chunk 61 optimal weight: 5.9990 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 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.233129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.201972 restraints weight = 14922.728| |-----------------------------------------------------------------------------| r_work (start): 0.4496 rms_B_bonded: 3.43 r_work: 0.4273 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10206 Z= 0.206 Angle : 0.674 9.895 13844 Z= 0.353 Chirality : 0.044 0.167 1538 Planarity : 0.006 0.068 1686 Dihedral : 6.652 54.523 1330 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 5.11 % Allowed : 22.96 % Favored : 71.93 % 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: -2.70 (0.24), residues: 1168 helix: -1.27 (0.18), residues: 716 sheet: -3.42 (0.76), residues: 26 loop : -2.41 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 629 HIS 0.004 0.001 HIS A 818 PHE 0.018 0.002 PHE A 556 TYR 0.031 0.001 TYR B 528 ARG 0.008 0.000 ARG B 753 *********************** 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 222 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 167 time to evaluate : 0.984 Fit side-chains REVERT: A 275 HIS cc_start: 0.6457 (OUTLIER) cc_final: 0.5393 (t-90) REVERT: A 298 ILE cc_start: 0.8062 (tp) cc_final: 0.7713 (tt) REVERT: A 377 PHE cc_start: 0.3407 (OUTLIER) cc_final: 0.3096 (t80) REVERT: A 403 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7491 (tm-30) REVERT: A 565 SER cc_start: 0.7538 (OUTLIER) cc_final: 0.7169 (p) REVERT: A 586 TYR cc_start: 0.5126 (OUTLIER) cc_final: 0.3919 (t80) REVERT: A 595 GLU cc_start: 0.6657 (mp0) cc_final: 0.6320 (mp0) REVERT: A 666 TYR cc_start: 0.8718 (m-10) cc_final: 0.8476 (m-80) REVERT: A 730 GLN cc_start: 0.7623 (mm-40) cc_final: 0.7410 (mp10) REVERT: A 742 MET cc_start: 0.8212 (tpp) cc_final: 0.7895 (mmt) REVERT: B 101 TYR cc_start: 0.6436 (t80) cc_final: 0.6034 (t80) REVERT: B 138 TYR cc_start: 0.5207 (m-80) cc_final: 0.4933 (m-80) REVERT: B 270 TYR cc_start: 0.5079 (t80) cc_final: 0.4830 (t80) REVERT: B 275 HIS cc_start: 0.6816 (OUTLIER) cc_final: 0.6083 (t-90) REVERT: B 298 ILE cc_start: 0.8072 (tp) cc_final: 0.7720 (tt) REVERT: B 394 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7600 (mm) REVERT: B 403 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7425 (tm-30) REVERT: B 565 SER cc_start: 0.7398 (OUTLIER) cc_final: 0.7146 (t) REVERT: B 586 TYR cc_start: 0.4951 (OUTLIER) cc_final: 0.3961 (t80) REVERT: B 742 MET cc_start: 0.8118 (tpp) cc_final: 0.7738 (mmt) REVERT: B 768 HIS cc_start: 0.4565 (t-90) cc_final: 0.4218 (t-90) outliers start: 55 outliers final: 34 residues processed: 210 average time/residue: 0.1800 time to fit residues: 56.1952 Evaluate side-chains 195 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 153 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE 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 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 504 THR Chi-restraints excluded: chain A residue 565 SER 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 352 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 504 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 586 TYR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 34 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 23 optimal weight: 0.0670 chunk 35 optimal weight: 0.3980 chunk 47 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 = 0.4860 r_free = 0.4860 target = 0.236431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.206512 restraints weight = 15247.969| |-----------------------------------------------------------------------------| r_work (start): 0.4547 rms_B_bonded: 3.38 r_work: 0.4322 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.4322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10206 Z= 0.190 Angle : 0.675 13.850 13844 Z= 0.352 Chirality : 0.044 0.163 1538 Planarity : 0.006 0.067 1686 Dihedral : 6.510 52.371 1330 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 4.37 % Allowed : 24.63 % Favored : 71.00 % 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: -2.48 (0.24), residues: 1168 helix: -1.01 (0.19), residues: 710 sheet: -3.31 (0.77), residues: 26 loop : -2.48 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 629 HIS 0.003 0.001 HIS A 818 PHE 0.022 0.002 PHE B 558 TYR 0.041 0.001 TYR B 528 ARG 0.009 0.000 ARG B 753 *********************** 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 216 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 169 time to evaluate : 1.159 Fit side-chains REVERT: A 275 HIS cc_start: 0.6328 (OUTLIER) cc_final: 0.5658 (t-90) REVERT: A 298 ILE cc_start: 0.8014 (tp) cc_final: 0.7695 (tt) REVERT: A 377 PHE cc_start: 0.3080 (OUTLIER) cc_final: 0.2795 (t80) REVERT: A 565 SER cc_start: 0.7145 (OUTLIER) cc_final: 0.6831 (p) REVERT: A 586 TYR cc_start: 0.5094 (OUTLIER) cc_final: 0.3996 (t80) REVERT: A 595 GLU cc_start: 0.6547 (mp0) cc_final: 0.6268 (mp0) REVERT: A 629 TRP cc_start: 0.5648 (m-90) cc_final: 0.5307 (m-90) REVERT: A 730 GLN cc_start: 0.7611 (mm-40) cc_final: 0.7331 (mp10) REVERT: A 742 MET cc_start: 0.8320 (tpp) cc_final: 0.7960 (mmt) REVERT: B 101 TYR cc_start: 0.6305 (t80) cc_final: 0.5927 (t80) REVERT: B 138 TYR cc_start: 0.5214 (m-80) cc_final: 0.4795 (m-80) REVERT: B 270 TYR cc_start: 0.4787 (t80) cc_final: 0.4564 (t80) REVERT: B 275 HIS cc_start: 0.6571 (OUTLIER) cc_final: 0.5896 (t-90) REVERT: B 298 ILE cc_start: 0.8015 (tp) cc_final: 0.7666 (tt) REVERT: B 394 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7600 (mm) REVERT: B 586 TYR cc_start: 0.4891 (OUTLIER) cc_final: 0.3984 (t80) REVERT: B 659 MET cc_start: 0.6572 (ttp) cc_final: 0.6303 (ttp) REVERT: B 742 MET cc_start: 0.8209 (tpp) cc_final: 0.7805 (mmt) REVERT: B 768 HIS cc_start: 0.4363 (t-90) cc_final: 0.4139 (t-90) outliers start: 47 outliers final: 35 residues processed: 205 average time/residue: 0.1902 time to fit residues: 57.3000 Evaluate side-chains 192 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE 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 381 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 565 SER 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 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 352 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 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: 1.9990 chunk 14 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 77 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 53 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 696 ASN ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN B 283 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 = 0.4833 r_free = 0.4833 target = 0.233147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.202631 restraints weight = 15033.798| |-----------------------------------------------------------------------------| r_work (start): 0.4507 rms_B_bonded: 3.30 r_work: 0.4275 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10206 Z= 0.250 Angle : 0.730 15.541 13844 Z= 0.376 Chirality : 0.045 0.162 1538 Planarity : 0.006 0.068 1686 Dihedral : 6.574 51.216 1330 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 5.30 % Allowed : 24.81 % 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: -2.39 (0.24), residues: 1168 helix: -1.00 (0.18), residues: 716 sheet: -3.43 (0.76), residues: 26 loop : -2.34 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 629 HIS 0.004 0.001 HIS A 818 PHE 0.025 0.002 PHE A 382 TYR 0.040 0.002 TYR A 528 ARG 0.006 0.000 ARG B 753 *********************** 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 207 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 150 time to evaluate : 1.061 Fit side-chains REVERT: A 275 HIS cc_start: 0.6487 (OUTLIER) cc_final: 0.5955 (t-90) REVERT: A 298 ILE cc_start: 0.8027 (tp) cc_final: 0.7694 (tt) REVERT: A 377 PHE cc_start: 0.3348 (OUTLIER) cc_final: 0.2969 (t80) REVERT: A 565 SER cc_start: 0.7232 (OUTLIER) cc_final: 0.6933 (p) REVERT: A 586 TYR cc_start: 0.5119 (OUTLIER) cc_final: 0.4013 (t80) REVERT: A 595 GLU cc_start: 0.6714 (mp0) cc_final: 0.6367 (mp0) REVERT: A 730 GLN cc_start: 0.7697 (mm-40) cc_final: 0.7409 (mp10) REVERT: A 742 MET cc_start: 0.8378 (tpp) cc_final: 0.8019 (mmt) REVERT: B 138 TYR cc_start: 0.5204 (m-80) cc_final: 0.4768 (m-80) REVERT: B 298 ILE cc_start: 0.8039 (tp) cc_final: 0.7665 (tt) REVERT: B 394 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7665 (mm) REVERT: B 478 ARG cc_start: 0.6219 (mmt90) cc_final: 0.4858 (mmp80) REVERT: B 565 SER cc_start: 0.7339 (OUTLIER) cc_final: 0.7130 (t) REVERT: B 586 TYR cc_start: 0.4892 (OUTLIER) cc_final: 0.3928 (t80) REVERT: B 730 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7570 (mp10) REVERT: B 742 MET cc_start: 0.8250 (tpp) cc_final: 0.7857 (mmt) outliers start: 57 outliers final: 39 residues processed: 194 average time/residue: 0.1983 time to fit residues: 56.1886 Evaluate side-chains 188 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 142 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE 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 381 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 565 SER 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 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 288 ILE Chi-restraints excluded: chain B residue 352 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 53 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 2 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 76 optimal weight: 0.0170 chunk 100 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 726 GLN ** 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 = 0.4849 r_free = 0.4849 target = 0.235366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.205290 restraints weight = 14981.082| |-----------------------------------------------------------------------------| r_work (start): 0.4534 rms_B_bonded: 3.29 r_work: 0.4307 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.4307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10206 Z= 0.200 Angle : 0.720 16.635 13844 Z= 0.365 Chirality : 0.045 0.208 1538 Planarity : 0.006 0.067 1686 Dihedral : 6.312 50.807 1328 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 4.37 % Allowed : 25.37 % Favored : 70.26 % 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: -2.24 (0.24), residues: 1168 helix: -0.86 (0.18), residues: 716 sheet: -3.26 (0.78), residues: 26 loop : -2.33 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 629 HIS 0.004 0.001 HIS A 818 PHE 0.031 0.002 PHE B 556 TYR 0.024 0.001 TYR A 569 ARG 0.008 0.000 ARG B 753 *********************** 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 202 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 155 time to evaluate : 1.056 Fit side-chains revert: symmetry clash REVERT: A 101 TYR cc_start: 0.6739 (m-80) cc_final: 0.6301 (m-80) REVERT: A 275 HIS cc_start: 0.6323 (OUTLIER) cc_final: 0.5981 (t-90) REVERT: A 298 ILE cc_start: 0.7954 (tp) cc_final: 0.7600 (tt) REVERT: A 377 PHE cc_start: 0.3027 (OUTLIER) cc_final: 0.2698 (t80) REVERT: A 528 TYR cc_start: 0.7073 (m-80) cc_final: 0.6872 (m-80) REVERT: A 565 SER cc_start: 0.7095 (OUTLIER) cc_final: 0.6852 (p) REVERT: A 586 TYR cc_start: 0.4917 (OUTLIER) cc_final: 0.3907 (t80) REVERT: A 595 GLU cc_start: 0.6646 (mp0) cc_final: 0.6352 (mp0) REVERT: A 730 GLN cc_start: 0.7689 (mm-40) cc_final: 0.7410 (mp10) REVERT: A 742 MET cc_start: 0.8240 (tpp) cc_final: 0.7900 (mmt) REVERT: B 138 TYR cc_start: 0.5236 (m-80) cc_final: 0.4788 (m-80) REVERT: B 298 ILE cc_start: 0.7988 (tp) cc_final: 0.7603 (tt) REVERT: B 394 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7639 (mm) REVERT: B 586 TYR cc_start: 0.4776 (OUTLIER) cc_final: 0.4082 (t80) REVERT: B 730 GLN cc_start: 0.7710 (mm-40) cc_final: 0.7494 (mp10) REVERT: B 742 MET cc_start: 0.8184 (tpp) cc_final: 0.7798 (mmt) outliers start: 47 outliers final: 36 residues processed: 191 average time/residue: 0.2048 time to fit residues: 56.4856 Evaluate side-chains 187 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 145 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 381 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 565 SER 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 288 ILE Chi-restraints excluded: chain B residue 352 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 586 TYR 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 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: 1.9990 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 96 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN B 726 GLN ** 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 = 0.4855 r_free = 0.4855 target = 0.235953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.207263 restraints weight = 15019.532| |-----------------------------------------------------------------------------| r_work (start): 0.4561 rms_B_bonded: 3.28 r_work: 0.4323 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.4323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10206 Z= 0.206 Angle : 0.715 15.148 13844 Z= 0.366 Chirality : 0.045 0.234 1538 Planarity : 0.006 0.067 1686 Dihedral : 6.209 49.022 1328 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 4.18 % Allowed : 25.74 % Favored : 70.07 % 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: -2.12 (0.24), residues: 1168 helix: -0.76 (0.19), residues: 716 sheet: -3.28 (0.77), residues: 26 loop : -2.28 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 629 HIS 0.004 0.001 HIS A 818 PHE 0.052 0.002 PHE A 573 TYR 0.025 0.001 TYR A 569 ARG 0.005 0.000 ARG B 753 ********************** 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 195 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 150 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 TYR cc_start: 0.6794 (m-80) cc_final: 0.6318 (m-80) REVERT: A 298 ILE cc_start: 0.7968 (tp) cc_final: 0.7625 (tt) REVERT: A 377 PHE cc_start: 0.3120 (OUTLIER) cc_final: 0.2874 (t80) REVERT: A 524 LEU cc_start: 0.7961 (tt) cc_final: 0.7708 (pp) REVERT: A 565 SER cc_start: 0.7018 (OUTLIER) cc_final: 0.6800 (p) REVERT: A 586 TYR cc_start: 0.4845 (OUTLIER) cc_final: 0.3864 (t80) REVERT: A 595 GLU cc_start: 0.6696 (mp0) cc_final: 0.6375 (mp0) REVERT: A 629 TRP cc_start: 0.5969 (m-90) cc_final: 0.5626 (m-90) REVERT: A 730 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7452 (mp10) REVERT: A 742 MET cc_start: 0.8200 (tpp) cc_final: 0.7852 (mmt) REVERT: B 101 TYR cc_start: 0.7191 (m-80) cc_final: 0.6984 (m-80) REVERT: B 138 TYR cc_start: 0.5256 (m-80) cc_final: 0.4860 (m-80) REVERT: B 298 ILE cc_start: 0.8053 (tp) cc_final: 0.7693 (tt) REVERT: B 394 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7685 (mm) REVERT: B 527 ILE cc_start: 0.9055 (mm) cc_final: 0.8791 (mt) REVERT: B 586 TYR cc_start: 0.4732 (OUTLIER) cc_final: 0.4064 (t80) REVERT: B 730 GLN cc_start: 0.7789 (mm-40) cc_final: 0.7571 (mp10) REVERT: B 742 MET cc_start: 0.8177 (tpp) cc_final: 0.7781 (mmt) outliers start: 45 outliers final: 35 residues processed: 185 average time/residue: 0.1814 time to fit residues: 49.8797 Evaluate side-chains 188 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 148 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 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 381 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 586 TYR 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 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 288 ILE Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 379 THR 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 586 TYR 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 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: 2.9990 chunk 34 optimal weight: 4.9990 chunk 77 optimal weight: 0.0030 chunk 57 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 14 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 50 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 726 GLN ** 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 = 0.4862 r_free = 0.4862 target = 0.236899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.207712 restraints weight = 15008.586| |-----------------------------------------------------------------------------| r_work (start): 0.4569 rms_B_bonded: 2.97 r_work: 0.4337 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.4337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10206 Z= 0.194 Angle : 0.716 14.121 13844 Z= 0.367 Chirality : 0.045 0.226 1538 Planarity : 0.006 0.075 1686 Dihedral : 5.950 45.526 1326 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 4.18 % Allowed : 26.58 % 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: -2.05 (0.24), residues: 1168 helix: -0.69 (0.19), residues: 716 sheet: -3.22 (0.79), residues: 26 loop : -2.28 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 629 HIS 0.004 0.001 HIS A 275 PHE 0.032 0.002 PHE B 556 TYR 0.021 0.001 TYR A 569 ARG 0.006 0.000 ARG B 753 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5293.84 seconds wall clock time: 94 minutes 50.91 seconds (5690.91 seconds total)