Starting phenix.real_space_refine on Fri Sep 11 13:29:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6p49_20247/09_2026/6p49_20247.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p49_20247/09_2026/6p49_20247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6p49_20247/09_2026/6p49_20247.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p49_20247/09_2026/6p49_20247.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6p49_20247/09_2026/6p49_20247.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6p49_20247/09_2026/6p49_20247.cif" model { file = "/net/cci-nas-00/data/ceres_data/6p49_20247/09_2026/6p49_20247.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p49_20247/09_2026/6p49_20247.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 66 5.16 5 C 6352 2.51 5 N 1520 2.21 5 O 1636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9576 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4787 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 556} Chain breaks: 8 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: 4.38, per 1000 atoms: 0.46 Number of scatterers: 9576 At special positions: 0 Unit cell: (84.72, 111.195, 106.959, 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 66 16.00 O 1636 8.00 N 1520 7.00 C 6352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.05 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=2.01 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=1.84 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.05 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 356 " distance=2.01 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=1.84 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: 0.66 Conformation dependent library (CDL) restraints added in 304.8 milliseconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2212 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 2 sheets defined 55.4% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 94 through 100 removed outlier: 3.724A pdb=" N ALA A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.724A pdb=" N TYR A 138 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 218 removed outlier: 3.573A pdb=" N TYR A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 Processing helix chain 'A' and resid 267 through 271 Processing helix chain 'A' and resid 284 through 292 removed outlier: 4.026A pdb=" N ILE A 288 " --> pdb=" O PRO A 284 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A 290 " --> pdb=" O ASP A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 327 removed outlier: 3.618A pdb=" N TRP A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY A 304 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA A 313 " --> pdb=" O MET A 309 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N CYS A 320 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE A 321 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY A 324 " --> pdb=" O CYS A 320 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP A 327 " --> pdb=" O TYR A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 378 through 408 removed outlier: 3.871A pdb=" N VAL A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE A 385 " --> pdb=" O ILE A 381 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLU A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 461 Processing helix chain 'A' and resid 462 through 480 removed outlier: 3.767A pdb=" N LEU A 466 " --> pdb=" O PHE A 462 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE A 475 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL A 476 " --> pdb=" O ILE A 472 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TYR A 477 " --> pdb=" O GLY A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 486 removed outlier: 3.558A pdb=" N SER A 486 " --> pdb=" O PHE A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 529 removed outlier: 3.824A pdb=" N SER A 514 " --> pdb=" O SER A 510 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 537 Processing helix chain 'A' and resid 547 through 563 removed outlier: 3.937A pdb=" N MET A 553 " --> pdb=" O ASN A 549 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N PHE A 556 " --> pdb=" O THR A 552 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LEU A 557 " --> pdb=" O MET A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 589 removed outlier: 3.619A pdb=" N LEU A 588 " --> pdb=" O VAL A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 614 removed outlier: 4.377A pdb=" N GLN A 608 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 627 Processing helix chain 'A' and resid 637 through 642 removed outlier: 3.835A pdb=" N GLY A 642 " --> pdb=" O LYS A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 676 removed outlier: 4.478A pdb=" N MET A 671 " --> pdb=" O GLU A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 709 removed outlier: 4.064A pdb=" N ILE A 700 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA A 704 " --> pdb=" O ILE A 700 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 707 " --> pdb=" O ASP A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 747 removed outlier: 4.171A pdb=" N LEU A 735 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 759 removed outlier: 3.617A pdb=" N TYR A 756 " --> pdb=" O PRO A 752 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR A 757 " --> pdb=" O ARG A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 839 removed outlier: 3.587A pdb=" N TRP A 829 " --> pdb=" O ASN A 825 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A 837 " --> pdb=" O ALA A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 845 Processing helix chain 'A' and resid 845 through 853 Processing helix chain 'B' and resid 94 through 100 removed outlier: 3.724A pdb=" N ALA B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.724A pdb=" N TYR B 138 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 218 removed outlier: 3.573A pdb=" N TYR B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 267 through 271 Processing helix chain 'B' and resid 284 through 292 removed outlier: 4.026A pdb=" N ILE B 288 " --> pdb=" O PRO B 284 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS B 290 " --> pdb=" O ASP B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 327 removed outlier: 3.617A pdb=" N TRP B 302 " --> pdb=" O ILE B 298 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY B 304 " --> pdb=" O PHE B 300 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA B 313 " --> pdb=" O MET B 309 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N CYS B 320 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE B 321 " --> pdb=" O GLY B 317 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY B 324 " --> pdb=" O CYS B 320 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP B 327 " --> pdb=" O TYR B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 378 through 408 removed outlier: 3.871A pdb=" N VAL B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE B 385 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLU B 395 " --> pdb=" O THR B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 461 Processing helix chain 'B' and resid 462 through 480 removed outlier: 3.767A pdb=" N LEU B 466 " --> pdb=" O PHE B 462 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE B 475 " --> pdb=" O VAL B 471 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL B 476 " --> pdb=" O ILE B 472 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TYR B 477 " --> pdb=" O GLY B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 486 removed outlier: 3.558A pdb=" N SER B 486 " --> pdb=" O PHE B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 529 removed outlier: 3.824A pdb=" N SER B 514 " --> pdb=" O SER B 510 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 537 Processing helix chain 'B' and resid 547 through 563 removed outlier: 3.937A pdb=" N MET B 553 " --> pdb=" O ASN B 549 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N PHE B 556 " --> pdb=" O THR B 552 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LEU B 557 " --> pdb=" O MET B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 589 removed outlier: 3.619A pdb=" N LEU B 588 " --> pdb=" O VAL B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 614 removed outlier: 4.377A pdb=" N GLN B 608 " --> pdb=" O GLU B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 627 Processing helix chain 'B' and resid 637 through 642 removed outlier: 3.834A pdb=" N GLY B 642 " --> pdb=" O LYS B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 removed outlier: 4.479A pdb=" N MET B 671 " --> pdb=" O GLU B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 709 removed outlier: 4.063A pdb=" N ILE B 700 " --> pdb=" O ASN B 696 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA B 704 " --> pdb=" O ILE B 700 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 707 " --> pdb=" O ASP B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 747 removed outlier: 4.171A pdb=" N LEU B 735 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 759 removed outlier: 3.617A pdb=" N TYR B 756 " --> pdb=" O PRO B 752 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR B 757 " --> pdb=" O ARG B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 839 removed outlier: 3.586A pdb=" N TRP B 829 " --> pdb=" O ASN B 825 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA B 837 " --> pdb=" O ALA B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 845 Processing helix chain 'B' and resid 845 through 853 Processing sheet with id=AA1, first strand: chain 'A' and resid 782 through 783 removed outlier: 3.770A pdb=" N SER A 782 " --> pdb=" O TYR A 809 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 782 through 783 removed outlier: 3.770A pdb=" N SER B 782 " --> pdb=" O TYR B 809 " (cutoff:3.500A) 362 hydrogen bonds defined for protein. 1062 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: 1.30 Time building geometry restraints manager: 0.96 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: 2795 1.34 - 1.46: 2362 1.46 - 1.58: 4581 1.58 - 1.70: 0 1.70 - 1.81: 104 Bond restraints: 9842 Sorted by residual: bond pdb=" C THR B 504 " pdb=" N PRO B 505 " ideal model delta sigma weight residual 1.334 1.401 -0.067 2.34e-02 1.83e+03 8.22e+00 bond pdb=" C THR A 504 " pdb=" N PRO A 505 " ideal model delta sigma weight residual 1.334 1.400 -0.066 2.34e-02 1.83e+03 8.03e+00 bond pdb=" C PRO A 763 " pdb=" N PRO A 764 " ideal model delta sigma weight residual 1.333 1.361 -0.028 1.01e-02 9.80e+03 7.68e+00 bond pdb=" C PRO B 763 " pdb=" N PRO B 764 " ideal model delta sigma weight residual 1.333 1.361 -0.028 1.01e-02 9.80e+03 7.56e+00 bond pdb=" N PRO A 686 " pdb=" CD PRO A 686 " ideal model delta sigma weight residual 1.473 1.511 -0.038 1.40e-02 5.10e+03 7.31e+00 ... (remaining 9837 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 12702 3.04 - 6.09: 519 6.09 - 9.13: 107 9.13 - 12.18: 18 12.18 - 15.22: 14 Bond angle restraints: 13360 Sorted by residual: angle pdb=" N VAL B 682 " pdb=" CA VAL B 682 " pdb=" C VAL B 682 " ideal model delta sigma weight residual 106.21 120.75 -14.54 1.07e+00 8.73e-01 1.85e+02 angle pdb=" N VAL A 682 " pdb=" CA VAL A 682 " pdb=" C VAL A 682 " ideal model delta sigma weight residual 106.21 120.74 -14.53 1.07e+00 8.73e-01 1.84e+02 angle pdb=" N GLN B 720 " pdb=" CA GLN B 720 " pdb=" C GLN B 720 " ideal model delta sigma weight residual 111.14 124.92 -13.78 1.08e+00 8.57e-01 1.63e+02 angle pdb=" N GLN A 720 " pdb=" CA GLN A 720 " pdb=" C GLN A 720 " ideal model delta sigma weight residual 111.14 124.88 -13.74 1.08e+00 8.57e-01 1.62e+02 angle pdb=" N ARG A 478 " pdb=" CA ARG A 478 " pdb=" C ARG A 478 " ideal model delta sigma weight residual 113.43 98.21 15.22 1.26e+00 6.30e-01 1.46e+02 ... (remaining 13355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4989 17.97 - 35.95: 607 35.95 - 53.92: 122 53.92 - 71.89: 22 71.89 - 89.87: 12 Dihedral angle restraints: 5752 sinusoidal: 2312 harmonic: 3440 Sorted by residual: dihedral pdb=" CB CYS A 596 " pdb=" SG CYS A 596 " pdb=" SG CYS A 601 " pdb=" CB CYS A 601 " ideal model delta sinusoidal sigma weight residual -86.00 -163.44 77.44 1 1.00e+01 1.00e-02 7.51e+01 dihedral pdb=" CB CYS B 596 " pdb=" SG CYS B 596 " pdb=" SG CYS B 601 " pdb=" CB CYS B 601 " ideal model delta sinusoidal sigma weight residual -86.00 -163.38 77.38 1 1.00e+01 1.00e-02 7.50e+01 dihedral pdb=" CB CYS B 338 " pdb=" SG CYS B 338 " pdb=" SG CYS B 365 " pdb=" CB CYS B 365 " ideal model delta sinusoidal sigma weight residual -86.00 -149.79 63.79 1 1.00e+01 1.00e-02 5.36e+01 ... (remaining 5749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 1339 0.122 - 0.243: 114 0.243 - 0.364: 17 0.364 - 0.486: 8 0.486 - 0.607: 2 Chirality restraints: 1480 Sorted by residual: chirality pdb=" CB VAL B 640 " pdb=" CA VAL B 640 " pdb=" CG1 VAL B 640 " pdb=" CG2 VAL B 640 " both_signs ideal model delta sigma weight residual False -2.63 -2.02 -0.61 2.00e-01 2.50e+01 9.21e+00 chirality pdb=" CB VAL A 640 " pdb=" CA VAL A 640 " pdb=" CG1 VAL A 640 " pdb=" CG2 VAL A 640 " both_signs ideal model delta sigma weight residual False -2.63 -2.02 -0.61 2.00e-01 2.50e+01 9.15e+00 chirality pdb=" CA ASP B 749 " pdb=" N ASP B 749 " pdb=" C ASP B 749 " pdb=" CB ASP B 749 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.21e+00 ... (remaining 1477 not shown) Planarity restraints: 1630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 719 " -0.025 2.00e-02 2.50e+03 4.97e-02 2.47e+01 pdb=" C ALA A 719 " 0.086 2.00e-02 2.50e+03 pdb=" O ALA A 719 " -0.033 2.00e-02 2.50e+03 pdb=" N GLN A 720 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 719 " -0.025 2.00e-02 2.50e+03 4.95e-02 2.45e+01 pdb=" C ALA B 719 " 0.086 2.00e-02 2.50e+03 pdb=" O ALA B 719 " -0.033 2.00e-02 2.50e+03 pdb=" N GLN B 720 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 688 " 0.066 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO B 689 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO B 689 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO B 689 " 0.056 5.00e-02 4.00e+02 ... (remaining 1627 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 610 2.71 - 3.26: 9308 3.26 - 3.81: 15541 3.81 - 4.35: 19408 4.35 - 4.90: 30570 Nonbonded interactions: 75437 Sorted by model distance: nonbonded pdb=" O PRO B 628 " pdb=" O TRP B 629 " model vdw 2.164 3.040 nonbonded pdb=" O PRO A 628 " pdb=" O TRP A 629 " model vdw 2.164 3.040 nonbonded pdb=" CD1 TRP A 359 " pdb=" N ARG A 360 " model vdw 2.191 3.340 nonbonded pdb=" CD1 TRP B 359 " pdb=" N ARG B 360 " model vdw 2.191 3.340 nonbonded pdb=" OH TYR A 847 " pdb=" OH TYR B 847 " model vdw 2.221 3.040 ... (remaining 75432 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: 0.01 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: 1.370 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: 0.140 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 11.460 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5727 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.189 9850 Z= 0.377 Angle : 1.585 39.996 13376 Z= 0.963 Chirality : 0.082 0.607 1480 Planarity : 0.010 0.101 1630 Dihedral : 16.183 89.867 3516 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.71 % Allowed : 6.90 % Favored : 92.39 % Rotamer: Outliers : 3.28 % Allowed : 10.23 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.27 (0.17), residues: 1130 helix: -4.42 (0.10), residues: 654 sheet: None (None), residues: 0 loop : -3.58 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 813 TYR 0.030 0.003 TYR A 306 PHE 0.030 0.003 PHE A 685 TRP 0.026 0.003 TRP A 302 HIS 0.006 0.002 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00697 / 0.35 ( 9842) covalent geometry : angle 1.50071 / 0.93 (13360) SS BOND : bond 0.09553 / 6.52 ( 8) SS BOND : angle 14.84253 / 9.51 ( 16) hydrogen bonds : bond 0.33047 / 20.97 ( 362) hydrogen bonds : angle 12.18805 / 8.31 ( 1062) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 553 MET cc_start: 0.5982 (mmm) cc_final: 0.5635 (mmt) REVERT: A 590 LYS cc_start: 0.4027 (OUTLIER) cc_final: 0.2742 (mmtt) REVERT: A 725 TRP cc_start: 0.6509 (m100) cc_final: 0.6083 (m100) REVERT: B 142 MET cc_start: 0.3547 (tpt) cc_final: 0.3199 (tpp) REVERT: B 553 MET cc_start: 0.5506 (mmm) cc_final: 0.5264 (mmt) REVERT: B 641 SER cc_start: 0.4003 (OUTLIER) cc_final: 0.3656 (t) outliers start: 34 outliers final: 10 residues processed: 222 average time/residue: 0.1017 time to fit residues: 30.7057 Evaluate side-chains 138 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 702 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.0070 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 275 HIS ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 ASN A 696 ASN A 730 GLN A 740 ASN A 814 ASN A 825 ASN B 275 HIS B 620 ASN B 621 ASN B 696 ASN B 730 GLN B 740 ASN B 814 ASN B 820 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5594 r_free = 0.5594 target = 0.279022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5348 r_free = 0.5348 target = 0.249823 restraints weight = 13036.779| |-----------------------------------------------------------------------------| r_work (start): 0.5307 rms_B_bonded: 2.49 r_work: 0.5125 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.5125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5852 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9850 Z= 0.174 Angle : 0.832 12.064 13376 Z= 0.430 Chirality : 0.047 0.193 1480 Planarity : 0.007 0.066 1630 Dihedral : 8.162 49.279 1300 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.32 % Favored : 91.50 % Rotamer: Outliers : 3.09 % Allowed : 17.18 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.32 (0.19), residues: 1130 helix: -3.27 (0.15), residues: 636 sheet: None (None), residues: 0 loop : -3.83 (0.22), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 592 TYR 0.022 0.002 TYR B 776 PHE 0.016 0.002 PHE A 556 TRP 0.021 0.002 TRP A 397 HIS 0.003 0.001 HIS A 824 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 ( 9842) covalent geometry : angle 0.83100 / 0.43 (13360) SS BOND : bond 0.01084 / 0.75 ( 8) SS BOND : angle 1.41263 / 0.84 ( 16) hydrogen bonds : bond 0.06700 / 4.24 ( 362) hydrogen bonds : angle 6.92458 / 4.66 ( 1062) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 LYS cc_start: 0.4158 (OUTLIER) cc_final: 0.2736 (mmtt) REVERT: A 598 PRO cc_start: 0.7141 (Cg_endo) cc_final: 0.6910 (Cg_exo) REVERT: A 634 ILE cc_start: 0.6370 (OUTLIER) cc_final: 0.6140 (pt) REVERT: B 268 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.7042 (pp) REVERT: B 553 MET cc_start: 0.6936 (mmm) cc_final: 0.6720 (tpt) REVERT: B 641 SER cc_start: 0.4081 (OUTLIER) cc_final: 0.3556 (t) REVERT: B 764 PRO cc_start: 0.6999 (Cg_endo) cc_final: 0.6699 (Cg_exo) outliers start: 32 outliers final: 16 residues processed: 184 average time/residue: 0.0861 time to fit residues: 22.7232 Evaluate side-chains 144 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain B residue 845 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 111 optimal weight: 0.0370 chunk 25 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 0.3980 chunk 35 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 20 optimal weight: 0.4980 chunk 79 optimal weight: 0.0020 chunk 95 optimal weight: 0.6980 overall best weight: 0.3266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 830 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5617 r_free = 0.5617 target = 0.282438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5369 r_free = 0.5369 target = 0.252468 restraints weight = 12927.953| |-----------------------------------------------------------------------------| r_work (start): 0.5331 rms_B_bonded: 2.58 r_work: 0.5145 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.5145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5820 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9850 Z= 0.143 Angle : 0.737 15.323 13376 Z= 0.374 Chirality : 0.045 0.199 1480 Planarity : 0.006 0.064 1630 Dihedral : 7.058 41.105 1291 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.32 % Favored : 91.50 % Rotamer: Outliers : 3.47 % Allowed : 18.53 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.83 (0.20), residues: 1130 helix: -2.81 (0.16), residues: 656 sheet: None (None), residues: 0 loop : -3.71 (0.23), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 592 TYR 0.017 0.002 TYR B 776 PHE 0.021 0.001 PHE B 556 TRP 0.020 0.001 TRP A 397 HIS 0.012 0.001 HIS A 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 ( 9842) covalent geometry : angle 0.73678 / 0.37 (13360) SS BOND : bond 0.00280 / 0.18 ( 8) SS BOND : angle 1.15032 / 0.74 ( 16) hydrogen bonds : bond 0.05972 / 3.76 ( 362) hydrogen bonds : angle 6.16646 / 4.11 ( 1062) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 364 THR cc_start: 0.6011 (OUTLIER) cc_final: 0.5811 (m) REVERT: A 590 LYS cc_start: 0.4396 (OUTLIER) cc_final: 0.3082 (mmtt) REVERT: A 601 CYS cc_start: 0.6006 (OUTLIER) cc_final: 0.5425 (m) REVERT: A 818 HIS cc_start: 0.5286 (t-90) cc_final: 0.4859 (t-90) REVERT: B 553 MET cc_start: 0.6788 (mmm) cc_final: 0.6576 (tpt) REVERT: B 601 CYS cc_start: 0.6538 (OUTLIER) cc_final: 0.6243 (m) outliers start: 36 outliers final: 18 residues processed: 159 average time/residue: 0.0666 time to fit residues: 16.2420 Evaluate side-chains 148 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 747 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 41 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 101 optimal weight: 0.2980 chunk 49 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 47 optimal weight: 0.0870 chunk 5 optimal weight: 0.8980 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 608 GLN A 620 ASN A 830 HIS B 94 GLN B 330 ASN ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5584 r_free = 0.5584 target = 0.278600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5320 r_free = 0.5320 target = 0.247441 restraints weight = 12923.711| |-----------------------------------------------------------------------------| r_work (start): 0.5293 rms_B_bonded: 2.78 r_work: 0.5104 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.5104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5913 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9850 Z= 0.162 Angle : 0.744 18.285 13376 Z= 0.376 Chirality : 0.046 0.173 1480 Planarity : 0.006 0.064 1630 Dihedral : 6.712 39.747 1290 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.94 % Favored : 90.88 % Rotamer: Outliers : 3.76 % Allowed : 20.37 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.54 (0.20), residues: 1130 helix: -2.51 (0.17), residues: 654 sheet: None (None), residues: 0 loop : -3.70 (0.23), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 753 TYR 0.020 0.002 TYR B 528 PHE 0.025 0.002 PHE B 125 TRP 0.021 0.002 TRP A 302 HIS 0.006 0.001 HIS A 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 ( 9842) covalent geometry : angle 0.74381 / 0.38 (13360) SS BOND : bond 0.00163 / 0.11 ( 8) SS BOND : angle 0.94259 / 0.63 ( 16) hydrogen bonds : bond 0.05805 / 3.66 ( 362) hydrogen bonds : angle 5.96124 / 3.94 ( 1062) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 135 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 LYS cc_start: 0.4572 (OUTLIER) cc_final: 0.3320 (mmtt) REVERT: A 773 MET cc_start: 0.6491 (mmm) cc_final: 0.6234 (mmm) REVERT: A 818 HIS cc_start: 0.5345 (t-90) cc_final: 0.5094 (t-90) REVERT: B 404 LEU cc_start: 0.7387 (mt) cc_final: 0.6997 (pp) REVERT: B 524 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7920 (tp) REVERT: B 553 MET cc_start: 0.7058 (mmm) cc_final: 0.6849 (tpt) REVERT: B 562 ASN cc_start: 0.7321 (t0) cc_final: 0.7052 (m110) REVERT: B 725 TRP cc_start: 0.6288 (m100) cc_final: 0.5820 (m100) REVERT: B 764 PRO cc_start: 0.7154 (Cg_endo) cc_final: 0.6854 (Cg_exo) outliers start: 39 outliers final: 25 residues processed: 165 average time/residue: 0.0683 time to fit residues: 17.3242 Evaluate side-chains 151 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 463 TRP Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 747 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 6 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 80 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 48 optimal weight: 0.1980 chunk 71 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 608 GLN ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN B 559 GLN ** B 620 ASN ** 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 = 0.5594 r_free = 0.5594 target = 0.280052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5335 r_free = 0.5335 target = 0.249342 restraints weight = 13033.416| |-----------------------------------------------------------------------------| r_work (start): 0.5309 rms_B_bonded: 2.75 r_work: 0.5120 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.5120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5898 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9850 Z= 0.147 Angle : 0.738 14.295 13376 Z= 0.369 Chirality : 0.045 0.182 1480 Planarity : 0.005 0.056 1630 Dihedral : 6.450 38.212 1288 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.03 % Favored : 90.80 % Rotamer: Outliers : 3.67 % Allowed : 21.72 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.31 (0.21), residues: 1130 helix: -2.30 (0.17), residues: 650 sheet: None (None), residues: 0 loop : -3.64 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 592 TYR 0.038 0.002 TYR A 528 PHE 0.020 0.001 PHE B 374 TRP 0.019 0.001 TRP B 463 HIS 0.005 0.001 HIS A 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 ( 9842) covalent geometry : angle 0.73755 / 0.37 (13360) SS BOND : bond 0.00139 / 0.09 ( 8) SS BOND : angle 0.75098 / 0.49 ( 16) hydrogen bonds : bond 0.05535 / 3.49 ( 362) hydrogen bonds : angle 5.78736 / 3.82 ( 1062) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 139 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 LYS cc_start: 0.4591 (OUTLIER) cc_final: 0.3471 (mmtm) REVERT: A 773 MET cc_start: 0.6457 (mmm) cc_final: 0.6207 (mmm) REVERT: B 142 MET cc_start: 0.3941 (tpp) cc_final: 0.3501 (tpp) REVERT: B 562 ASN cc_start: 0.7301 (t0) cc_final: 0.5973 (t0) REVERT: B 590 LYS cc_start: 0.5329 (OUTLIER) cc_final: 0.4227 (mmtm) REVERT: B 725 TRP cc_start: 0.6310 (m100) cc_final: 0.5864 (m100) REVERT: B 764 PRO cc_start: 0.6929 (Cg_endo) cc_final: 0.6596 (Cg_exo) outliers start: 38 outliers final: 29 residues processed: 170 average time/residue: 0.0707 time to fit residues: 18.1305 Evaluate side-chains 157 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 463 TRP Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 747 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 67 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 559 GLN A 608 GLN A 620 ASN A 710 GLN A 726 GLN A 844 HIS B 94 GLN ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5579 r_free = 0.5579 target = 0.277983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5319 r_free = 0.5319 target = 0.247128 restraints weight = 13012.142| |-----------------------------------------------------------------------------| r_work (start): 0.5294 rms_B_bonded: 2.79 r_work: 0.5095 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.5095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5926 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9850 Z= 0.153 Angle : 0.738 13.860 13376 Z= 0.373 Chirality : 0.046 0.253 1480 Planarity : 0.005 0.055 1630 Dihedral : 6.310 37.313 1287 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.20 % Favored : 90.62 % Rotamer: Outliers : 3.86 % Allowed : 22.10 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.14 (0.21), residues: 1130 helix: -2.13 (0.18), residues: 662 sheet: None (None), residues: 0 loop : -3.63 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 542 TYR 0.034 0.002 TYR A 528 PHE 0.026 0.002 PHE A 681 TRP 0.018 0.001 TRP B 397 HIS 0.004 0.001 HIS A 824 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 9842) covalent geometry : angle 0.73797 / 0.37 (13360) SS BOND : bond 0.00118 / 0.08 ( 8) SS BOND : angle 0.62986 / 0.42 ( 16) hydrogen bonds : bond 0.05525 / 3.52 ( 362) hydrogen bonds : angle 5.73205 / 3.77 ( 1062) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 TYR cc_start: 0.5722 (m-80) cc_final: 0.5449 (m-80) REVERT: A 590 LYS cc_start: 0.4608 (OUTLIER) cc_final: 0.3638 (mmtm) REVERT: A 604 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7206 (tp30) REVERT: B 590 LYS cc_start: 0.5371 (OUTLIER) cc_final: 0.4354 (mmtm) REVERT: B 725 TRP cc_start: 0.6414 (m100) cc_final: 0.5983 (m100) REVERT: B 764 PRO cc_start: 0.6928 (Cg_endo) cc_final: 0.6627 (Cg_exo) REVERT: B 773 MET cc_start: 0.5856 (mmm) cc_final: 0.5632 (mmm) REVERT: B 842 MET cc_start: 0.7450 (mmt) cc_final: 0.7033 (mmt) outliers start: 40 outliers final: 31 residues processed: 169 average time/residue: 0.0712 time to fit residues: 18.4254 Evaluate side-chains 159 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 463 TRP Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 463 TRP Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 747 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 87 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 65 optimal weight: 0.0020 chunk 99 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 608 GLN ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5584 r_free = 0.5584 target = 0.279554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5335 r_free = 0.5335 target = 0.249471 restraints weight = 13045.500| |-----------------------------------------------------------------------------| r_work (start): 0.5303 rms_B_bonded: 2.66 r_work: 0.5094 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.5094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5934 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9850 Z= 0.148 Angle : 0.757 13.470 13376 Z= 0.375 Chirality : 0.046 0.244 1480 Planarity : 0.005 0.056 1630 Dihedral : 6.215 36.507 1287 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.29 % Favored : 90.53 % Rotamer: Outliers : 4.15 % Allowed : 23.55 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.90 (0.22), residues: 1130 helix: -1.95 (0.18), residues: 658 sheet: None (None), residues: 0 loop : -3.50 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 542 TYR 0.038 0.002 TYR A 528 PHE 0.034 0.002 PHE B 851 TRP 0.019 0.001 TRP B 397 HIS 0.005 0.001 HIS A 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 ( 9842) covalent geometry : angle 0.75703 / 0.38 (13360) SS BOND : bond 0.00124 / 0.09 ( 8) SS BOND : angle 0.69450 / 0.46 ( 16) hydrogen bonds : bond 0.05363 / 3.41 ( 362) hydrogen bonds : angle 5.64542 / 3.70 ( 1062) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 132 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 LYS cc_start: 0.4977 (OUTLIER) cc_final: 0.4026 (mmtm) REVERT: A 604 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7222 (tp30) REVERT: B 386 MET cc_start: 0.5154 (mmt) cc_final: 0.4849 (mmt) REVERT: B 524 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7887 (tp) REVERT: B 590 LYS cc_start: 0.5323 (OUTLIER) cc_final: 0.4404 (mmtm) REVERT: B 725 TRP cc_start: 0.6362 (m100) cc_final: 0.5966 (m100) REVERT: B 749 ASP cc_start: 0.6116 (OUTLIER) cc_final: 0.5878 (m-30) REVERT: B 750 MET cc_start: 0.6937 (tpt) cc_final: 0.6716 (tpt) REVERT: B 764 PRO cc_start: 0.6876 (Cg_endo) cc_final: 0.6579 (Cg_exo) REVERT: B 842 MET cc_start: 0.7524 (mmt) cc_final: 0.7200 (mmt) outliers start: 43 outliers final: 34 residues processed: 167 average time/residue: 0.0713 time to fit residues: 18.0500 Evaluate side-chains 162 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 123 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 463 TRP Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 847 TYR Chi-restraints excluded: chain B residue 848 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 63 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 12 optimal weight: 0.1980 chunk 33 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 93 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 559 GLN A 608 GLN ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5564 r_free = 0.5564 target = 0.276558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.5310 r_free = 0.5310 target = 0.246175 restraints weight = 13085.620| |-----------------------------------------------------------------------------| r_work (start): 0.5278 rms_B_bonded: 3.19 r_work: 0.5048 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.5048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5999 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9850 Z= 0.165 Angle : 0.774 13.126 13376 Z= 0.388 Chirality : 0.047 0.210 1480 Planarity : 0.005 0.053 1630 Dihedral : 6.243 36.770 1287 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.91 % Favored : 89.91 % Rotamer: Outliers : 3.86 % Allowed : 24.13 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.81 (0.22), residues: 1130 helix: -1.87 (0.18), residues: 658 sheet: None (None), residues: 0 loop : -3.48 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 478 TYR 0.038 0.002 TYR A 528 PHE 0.022 0.002 PHE B 681 TRP 0.014 0.001 TRP B 397 HIS 0.005 0.001 HIS B 824 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 ( 9842) covalent geometry : angle 0.77446 / 0.39 (13360) SS BOND : bond 0.00129 / 0.08 ( 8) SS BOND : angle 0.67811 / 0.44 ( 16) hydrogen bonds : bond 0.05501 / 3.53 ( 362) hydrogen bonds : angle 5.70604 / 3.74 ( 1062) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 125 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 LYS cc_start: 0.5055 (OUTLIER) cc_final: 0.4101 (mmtm) REVERT: A 604 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7142 (tp30) REVERT: B 386 MET cc_start: 0.4773 (mmt) cc_final: 0.4481 (mmt) REVERT: B 524 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7614 (tp) REVERT: B 590 LYS cc_start: 0.5311 (OUTLIER) cc_final: 0.4418 (mmtm) REVERT: B 749 ASP cc_start: 0.6366 (OUTLIER) cc_final: 0.6083 (m-30) REVERT: B 764 PRO cc_start: 0.7051 (Cg_endo) cc_final: 0.6766 (Cg_exo) REVERT: B 842 MET cc_start: 0.7566 (mmt) cc_final: 0.7233 (mmt) outliers start: 40 outliers final: 28 residues processed: 160 average time/residue: 0.0660 time to fit residues: 16.2184 Evaluate side-chains 150 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 463 TRP Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 848 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 21 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 29 optimal weight: 0.0020 chunk 42 optimal weight: 2.9990 chunk 70 optimal weight: 0.3980 chunk 112 optimal weight: 0.6980 overall best weight: 1.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 559 GLN A 608 GLN A 620 ASN ** B 620 ASN ** 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 = 0.5558 r_free = 0.5558 target = 0.275833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5302 r_free = 0.5302 target = 0.244453 restraints weight = 12986.755| |-----------------------------------------------------------------------------| r_work (start): 0.5261 rms_B_bonded: 3.41 r_work: 0.5028 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.5028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6021 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9850 Z= 0.167 Angle : 0.786 13.453 13376 Z= 0.390 Chirality : 0.046 0.193 1480 Planarity : 0.005 0.057 1630 Dihedral : 6.185 35.646 1286 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.18 % Favored : 89.65 % Rotamer: Outliers : 3.47 % Allowed : 25.19 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.72 (0.22), residues: 1130 helix: -1.80 (0.18), residues: 668 sheet: None (None), residues: 0 loop : -3.45 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 478 TYR 0.035 0.002 TYR A 528 PHE 0.023 0.002 PHE A 681 TRP 0.019 0.001 TRP B 397 HIS 0.005 0.001 HIS A 824 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 ( 9842) covalent geometry : angle 0.78566 / 0.39 (13360) SS BOND : bond 0.00140 / 0.09 ( 8) SS BOND : angle 0.73339 / 0.47 ( 16) hydrogen bonds : bond 0.05486 / 3.49 ( 362) hydrogen bonds : angle 5.71126 / 3.73 ( 1062) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 MET cc_start: 0.5185 (mmt) cc_final: 0.4463 (mmt) REVERT: A 590 LYS cc_start: 0.5268 (OUTLIER) cc_final: 0.4365 (mmtt) REVERT: A 604 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7176 (tp30) REVERT: B 386 MET cc_start: 0.4706 (mmt) cc_final: 0.4359 (mmt) REVERT: B 534 MET cc_start: 0.7681 (tmm) cc_final: 0.7347 (mmm) REVERT: B 590 LYS cc_start: 0.5411 (OUTLIER) cc_final: 0.4621 (mmtt) REVERT: B 742 MET cc_start: 0.5653 (ptp) cc_final: 0.5443 (ptt) REVERT: B 749 ASP cc_start: 0.6056 (OUTLIER) cc_final: 0.5807 (m-30) REVERT: B 764 PRO cc_start: 0.7136 (Cg_endo) cc_final: 0.6877 (Cg_exo) REVERT: B 773 MET cc_start: 0.6307 (mmm) cc_final: 0.5873 (mmm) REVERT: B 842 MET cc_start: 0.7611 (mmt) cc_final: 0.7247 (mmt) outliers start: 36 outliers final: 26 residues processed: 152 average time/residue: 0.0641 time to fit residues: 15.3788 Evaluate side-chains 148 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 463 TRP Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 749 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 41 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 72 optimal weight: 0.3980 chunk 57 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 559 GLN A 608 GLN A 620 ASN B 559 GLN ** B 620 ASN ** 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 = 0.5582 r_free = 0.5582 target = 0.277894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5318 r_free = 0.5318 target = 0.247267 restraints weight = 12593.859| |-----------------------------------------------------------------------------| r_work (start): 0.5284 rms_B_bonded: 3.17 r_work: 0.5073 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.5073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5946 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9850 Z= 0.149 Angle : 0.769 12.970 13376 Z= 0.379 Chirality : 0.046 0.177 1480 Planarity : 0.005 0.054 1630 Dihedral : 6.025 34.956 1286 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 3.19 % Allowed : 25.97 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.54 (0.22), residues: 1130 helix: -1.65 (0.18), residues: 666 sheet: None (None), residues: 0 loop : -3.37 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 753 TYR 0.045 0.002 TYR B 828 PHE 0.021 0.001 PHE A 681 TRP 0.020 0.001 TRP B 397 HIS 0.003 0.001 HIS B 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 ( 9842) covalent geometry : angle 0.76932 / 0.38 (13360) SS BOND : bond 0.00101 / 0.07 ( 8) SS BOND : angle 0.68299 / 0.42 ( 16) hydrogen bonds : bond 0.05274 / 3.35 ( 362) hydrogen bonds : angle 5.56179 / 3.64 ( 1062) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 MET cc_start: 0.5119 (mmt) cc_final: 0.4363 (mmt) REVERT: A 553 MET cc_start: 0.7033 (mmt) cc_final: 0.6323 (mmt) REVERT: A 590 LYS cc_start: 0.5224 (OUTLIER) cc_final: 0.4397 (mmtt) REVERT: A 604 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7194 (tp30) REVERT: A 613 MET cc_start: 0.6461 (ttt) cc_final: 0.6192 (ttt) REVERT: A 729 MET cc_start: 0.6203 (ttp) cc_final: 0.5992 (ttp) REVERT: B 386 MET cc_start: 0.4745 (mmt) cc_final: 0.4365 (mmt) REVERT: B 524 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7605 (tp) REVERT: B 534 MET cc_start: 0.7581 (tmm) cc_final: 0.7246 (mmm) REVERT: B 590 LYS cc_start: 0.5563 (OUTLIER) cc_final: 0.4912 (mmtm) REVERT: B 764 PRO cc_start: 0.7052 (Cg_endo) cc_final: 0.6776 (Cg_exo) REVERT: B 773 MET cc_start: 0.6202 (mmm) cc_final: 0.5897 (mmm) REVERT: B 842 MET cc_start: 0.7445 (mmt) cc_final: 0.7145 (mmt) outliers start: 33 outliers final: 27 residues processed: 152 average time/residue: 0.0714 time to fit residues: 16.8148 Evaluate side-chains 145 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 463 TRP Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 768 HIS Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 747 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 51 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 113 optimal weight: 0.5980 chunk 86 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 GLN A 559 GLN A 620 ASN B 559 GLN B 620 ASN B 623 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5540 r_free = 0.5540 target = 0.272967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5267 r_free = 0.5267 target = 0.241604 restraints weight = 12574.008| |-----------------------------------------------------------------------------| r_work (start): 0.5233 rms_B_bonded: 3.03 r_work: 0.5016 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.5016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6063 moved from start: 0.5444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9850 Z= 0.198 Angle : 0.827 12.669 13376 Z= 0.411 Chirality : 0.048 0.184 1480 Planarity : 0.006 0.060 1630 Dihedral : 6.246 34.739 1286 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.15 % Favored : 88.85 % Rotamer: Outliers : 3.38 % Allowed : 26.06 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.63 (0.22), residues: 1130 helix: -1.73 (0.18), residues: 666 sheet: None (None), residues: 0 loop : -3.41 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 399 TYR 0.046 0.002 TYR B 828 PHE 0.023 0.002 PHE B 681 TRP 0.016 0.002 TRP B 397 HIS 0.006 0.001 HIS A 824 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.20 ( 9842) covalent geometry : angle 0.82667 / 0.41 (13360) SS BOND : bond 0.00159 / 0.10 ( 8) SS BOND : angle 0.75108 / 0.48 ( 16) hydrogen bonds : bond 0.05647 / 3.60 ( 362) hydrogen bonds : angle 5.77500 / 3.77 ( 1062) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2118.88 seconds wall clock time: 37 minutes 2.59 seconds (2222.59 seconds total)