Starting phenix.real_space_refine on Fri Feb 14 00:53:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6p49_20247/02_2025/6p49_20247.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p49_20247/02_2025/6p49_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_20247/02_2025/6p49_20247.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p49_20247/02_2025/6p49_20247.map" model { file = "/net/cci-nas-00/data/ceres_data/6p49_20247/02_2025/6p49_20247.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p49_20247/02_2025/6p49_20247.cif" } resolution = 3.3 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= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 8.72, per 1000 atoms: 0.91 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=4, 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 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: 2.38 Conformation dependent library (CDL) restraints added in 898.3 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: 0.95 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: 2.51 Time building geometry restraints manager: 2.77 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: 4983 17.97 - 35.95: 605 35.95 - 53.92: 121 53.92 - 71.89: 20 71.89 - 89.87: 11 Dihedral angle restraints: 5740 sinusoidal: 2300 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 A 338 " pdb=" SG CYS A 338 " pdb=" SG CYS A 365 " pdb=" CB CYS A 365 " ideal model delta sinusoidal sigma weight residual -86.00 -149.79 63.79 1 1.00e+01 1.00e-02 5.36e+01 dihedral pdb=" CB CYS A 352 " pdb=" SG CYS A 352 " pdb=" SG CYS A 356 " pdb=" CB CYS A 356 " ideal model delta sinusoidal sigma weight residual -86.00 -146.18 60.18 1 1.00e+01 1.00e-02 4.83e+01 ... (remaining 5737 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: 1.84 - 2.45: 61 2.45 - 3.07: 5750 3.07 - 3.68: 14980 3.68 - 4.29: 21242 4.29 - 4.90: 33416 Nonbonded interactions: 75449 Sorted by model distance: nonbonded pdb=" SG CYS B 596 " pdb=" SG CYS B 601 " model vdw 1.843 3.760 nonbonded pdb=" SG CYS B 352 " pdb=" SG CYS B 356 " model vdw 2.009 3.760 nonbonded pdb=" SG CYS B 349 " pdb=" SG CYS B 807 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS B 338 " pdb=" SG CYS B 365 " model vdw 2.053 3.760 nonbonded pdb=" O PRO B 628 " pdb=" O TRP B 629 " model vdw 2.164 3.040 ... (remaining 75444 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.920 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5705 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 0.067 9842 Z= 0.452 Angle : 1.501 15.220 13360 Z= 0.932 Chirality : 0.082 0.607 1480 Planarity : 0.010 0.101 1630 Dihedral : 16.183 89.867 3516 Min Nonbonded Distance : 1.843 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 (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: -6.27 (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 TRP 0.026 0.003 TRP A 302 HIS 0.006 0.002 HIS B 275 PHE 0.030 0.003 PHE A 685 TYR 0.030 0.003 TYR A 306 ARG 0.006 0.001 ARG A 813 *********************** 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 : 0.997 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: 0.2743 (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: 0.3650 (t) outliers start: 34 outliers final: 10 residues processed: 222 average time/residue: 0.2482 time to fit residues: 73.8764 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 : 1.037 ------------------------------------------------------------------------------- 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 97 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 830 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5586 r_free = 0.5586 target = 0.278178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5330 r_free = 0.5330 target = 0.247615 restraints weight = 13059.292| |-----------------------------------------------------------------------------| r_work (start): 0.5288 rms_B_bonded: 2.81 r_work: 0.5101 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.5101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5859 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9842 Z= 0.232 Angle : 0.838 12.273 13360 Z= 0.435 Chirality : 0.047 0.199 1480 Planarity : 0.007 0.067 1630 Dihedral : 8.288 49.182 1300 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.32 % Favored : 91.50 % Rotamer: Outliers : 2.80 % Allowed : 16.99 % Favored : 80.21 % Cbeta Deviations : 0.00 % 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: -5.36 (0.18), residues: 1130 helix: -3.31 (0.15), residues: 636 sheet: None (None), residues: 0 loop : -3.83 (0.22), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 397 HIS 0.004 0.001 HIS A 824 PHE 0.016 0.002 PHE A 556 TYR 0.021 0.002 TYR B 776 ARG 0.011 0.001 ARG B 592 *********************** 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 184 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 LYS cc_start: 0.4209 (OUTLIER) cc_final: 0.2643 (mmtt) REVERT: A 598 PRO cc_start: 0.7162 (Cg_endo) cc_final: 0.6930 (Cg_exo) REVERT: A 601 CYS cc_start: 0.6065 (OUTLIER) cc_final: 0.5540 (m) REVERT: A 634 ILE cc_start: 0.6395 (OUTLIER) cc_final: 0.6157 (pt) REVERT: B 268 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.7063 (pp) REVERT: B 641 SER cc_start: 0.4108 (OUTLIER) cc_final: 0.3579 (t) REVERT: B 764 PRO cc_start: 0.7001 (Cg_endo) cc_final: 0.6679 (Cg_exo) outliers start: 29 outliers final: 14 residues processed: 176 average time/residue: 0.2131 time to fit residues: 52.9454 Evaluate side-chains 146 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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 601 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 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 85 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 GLN A 830 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5568 r_free = 0.5568 target = 0.275529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5299 r_free = 0.5299 target = 0.244033 restraints weight = 13024.485| |-----------------------------------------------------------------------------| r_work (start): 0.5266 rms_B_bonded: 2.68 r_work: 0.5078 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.5078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5921 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9842 Z= 0.239 Angle : 0.775 15.110 13360 Z= 0.398 Chirality : 0.046 0.215 1480 Planarity : 0.006 0.060 1630 Dihedral : 7.355 41.602 1291 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.29 % Favored : 90.53 % Rotamer: Outliers : 3.47 % Allowed : 18.73 % Favored : 77.80 % Cbeta Deviations : 0.00 % 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: -4.93 (0.19), residues: 1130 helix: -2.93 (0.16), residues: 654 sheet: None (None), residues: 0 loop : -3.70 (0.23), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 397 HIS 0.006 0.001 HIS A 824 PHE 0.022 0.002 PHE A 556 TYR 0.022 0.002 TYR A 306 ARG 0.005 0.000 ARG A 753 *********************** 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 173 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 ARG cc_start: 0.6229 (mtt90) cc_final: 0.5768 (mpt-90) REVERT: A 590 LYS cc_start: 0.4472 (OUTLIER) cc_final: 0.3062 (mmtt) REVERT: A 598 PRO cc_start: 0.7148 (Cg_endo) cc_final: 0.6891 (Cg_exo) REVERT: B 364 THR cc_start: 0.6757 (OUTLIER) cc_final: 0.6390 (m) REVERT: B 742 MET cc_start: 0.5710 (mtp) cc_final: 0.5499 (mtt) outliers start: 36 outliers final: 23 residues processed: 165 average time/residue: 0.1858 time to fit residues: 45.1182 Evaluate side-chains 147 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 1.539 ------------------------------------------------------------------------------- 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 570 ILE Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 714 MET 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 268 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 364 THR 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 570 ILE Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 845 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 22 optimal weight: 1.9990 chunk 107 optimal weight: 0.1980 chunk 19 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 GLN A 620 ASN ** A 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN B 330 ASN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5570 r_free = 0.5570 target = 0.276890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5304 r_free = 0.5304 target = 0.245608 restraints weight = 12918.971| |-----------------------------------------------------------------------------| r_work (start): 0.5277 rms_B_bonded: 2.71 r_work: 0.5094 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.5094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5902 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9842 Z= 0.214 Angle : 0.734 12.236 13360 Z= 0.375 Chirality : 0.045 0.176 1480 Planarity : 0.005 0.058 1630 Dihedral : 6.880 39.498 1290 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.32 % Favored : 91.50 % Rotamer: Outliers : 3.86 % Allowed : 20.95 % Favored : 75.19 % Cbeta Deviations : 0.00 % 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: -4.58 (0.20), residues: 1130 helix: -2.55 (0.17), residues: 654 sheet: None (None), residues: 0 loop : -3.71 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 397 HIS 0.004 0.001 HIS A 824 PHE 0.027 0.002 PHE A 681 TYR 0.021 0.002 TYR A 306 ARG 0.003 0.000 ARG A 753 *********************** 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 172 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 LYS cc_start: 0.4602 (OUTLIER) cc_final: 0.3299 (mmtt) REVERT: A 598 PRO cc_start: 0.7145 (Cg_endo) cc_final: 0.6922 (Cg_exo) REVERT: A 725 TRP cc_start: 0.6266 (m100) cc_final: 0.6058 (m100) REVERT: B 404 LEU cc_start: 0.7386 (mt) cc_final: 0.6962 (pp) REVERT: B 524 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7964 (tp) REVERT: B 562 ASN cc_start: 0.7477 (t0) cc_final: 0.7130 (m110) REVERT: B 604 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7392 (tp30) REVERT: B 764 PRO cc_start: 0.7162 (Cg_endo) cc_final: 0.6860 (Cg_exo) outliers start: 40 outliers final: 26 residues processed: 161 average time/residue: 0.2041 time to fit residues: 49.0007 Evaluate side-chains 151 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 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 596 CYS Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 707 LEU 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 331 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 468 ILE 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 604 GLU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 845 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 20 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 73 optimal weight: 0.0470 chunk 70 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 GLN A 608 GLN A 710 GLN B 94 GLN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.5587 r_free = 0.5587 target = 0.279246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5331 r_free = 0.5331 target = 0.248606 restraints weight = 12850.341| |-----------------------------------------------------------------------------| r_work (start): 0.5304 rms_B_bonded: 2.74 r_work: 0.5114 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.5114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5868 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9842 Z= 0.185 Angle : 0.713 11.766 13360 Z= 0.360 Chirality : 0.045 0.181 1480 Planarity : 0.005 0.060 1630 Dihedral : 6.457 37.844 1288 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.94 % Favored : 90.88 % Rotamer: Outliers : 3.47 % Allowed : 22.20 % Favored : 74.32 % Cbeta Deviations : 0.00 % 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: -4.24 (0.21), residues: 1130 helix: -2.22 (0.18), residues: 652 sheet: None (None), residues: 0 loop : -3.65 (0.24), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 397 HIS 0.002 0.001 HIS A 824 PHE 0.025 0.002 PHE B 681 TYR 0.041 0.001 TYR A 528 ARG 0.003 0.000 ARG B 592 *********************** 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 176 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 TYR cc_start: 0.5962 (m-80) cc_final: 0.5244 (m-80) REVERT: A 562 ASN cc_start: 0.7153 (t0) cc_final: 0.6830 (t0) REVERT: A 590 LYS cc_start: 0.4677 (OUTLIER) cc_final: 0.3559 (mmtm) REVERT: A 725 TRP cc_start: 0.6298 (m100) cc_final: 0.6069 (m100) REVERT: B 142 MET cc_start: 0.4223 (tpp) cc_final: 0.3805 (tpp) REVERT: B 478 ARG cc_start: 0.6329 (mtt90) cc_final: 0.5889 (mpt-90) REVERT: B 562 ASN cc_start: 0.7401 (t0) cc_final: 0.6334 (t0) REVERT: B 590 LYS cc_start: 0.5428 (OUTLIER) cc_final: 0.4306 (mmtm) REVERT: B 725 TRP cc_start: 0.6390 (m100) cc_final: 0.5953 (m100) REVERT: B 764 PRO cc_start: 0.7081 (Cg_endo) cc_final: 0.6795 (Cg_exo) outliers start: 36 outliers final: 23 residues processed: 167 average time/residue: 0.2134 time to fit residues: 52.2248 Evaluate side-chains 152 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 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 611 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 654 TYR 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 382 PHE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 707 LEU 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 98 optimal weight: 0.9980 chunk 43 optimal weight: 0.0470 chunk 75 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 50 optimal weight: 0.1980 chunk 69 optimal weight: 0.9980 chunk 101 optimal weight: 0.2980 chunk 91 optimal weight: 3.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 GLN A 620 ASN A 726 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 = 0.279897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5341 r_free = 0.5341 target = 0.249530 restraints weight = 12907.325| |-----------------------------------------------------------------------------| r_work (start): 0.5317 rms_B_bonded: 2.80 r_work: 0.5127 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.5127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5836 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9842 Z= 0.187 Angle : 0.729 11.115 13360 Z= 0.363 Chirality : 0.045 0.224 1480 Planarity : 0.005 0.062 1630 Dihedral : 6.228 36.952 1287 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.50 % Favored : 91.33 % Rotamer: Outliers : 3.67 % Allowed : 22.59 % Favored : 73.75 % Cbeta Deviations : 0.00 % 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: -4.00 (0.22), residues: 1130 helix: -2.02 (0.18), residues: 660 sheet: None (None), residues: 0 loop : -3.56 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 397 HIS 0.002 0.001 HIS A 824 PHE 0.023 0.001 PHE A 681 TYR 0.028 0.001 TYR A 528 ARG 0.002 0.000 ARG B 592 *********************** 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 174 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 LYS cc_start: 0.4977 (OUTLIER) cc_final: 0.3957 (mmtm) REVERT: A 604 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7126 (tp30) REVERT: A 725 TRP cc_start: 0.6202 (m100) cc_final: 0.6001 (m100) REVERT: A 729 MET cc_start: 0.6320 (ttp) cc_final: 0.6118 (ttp) REVERT: B 142 MET cc_start: 0.4545 (tpp) cc_final: 0.4150 (tpp) REVERT: B 590 LYS cc_start: 0.5407 (OUTLIER) cc_final: 0.4421 (mmtm) REVERT: B 725 TRP cc_start: 0.6249 (m100) cc_final: 0.5867 (m100) REVERT: B 764 PRO cc_start: 0.6927 (Cg_endo) cc_final: 0.6613 (Cg_exo) outliers start: 38 outliers final: 22 residues processed: 168 average time/residue: 0.1913 time to fit residues: 46.9316 Evaluate side-chains 149 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 654 TYR Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 845 ILE 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 535 ILE Chi-restraints excluded: chain B residue 590 LYS 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 845 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 22 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 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 = 0.5586 r_free = 0.5586 target = 0.278641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5328 r_free = 0.5328 target = 0.247681 restraints weight = 12917.598| |-----------------------------------------------------------------------------| r_work (start): 0.5288 rms_B_bonded: 2.79 r_work: 0.5074 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.5074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5908 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9842 Z= 0.209 Angle : 0.750 10.001 13360 Z= 0.376 Chirality : 0.046 0.213 1480 Planarity : 0.005 0.061 1630 Dihedral : 6.200 36.359 1287 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.73 % Favored : 90.09 % Rotamer: Outliers : 3.86 % Allowed : 23.65 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.87 (0.22), residues: 1130 helix: -1.92 (0.18), residues: 664 sheet: None (None), residues: 0 loop : -3.51 (0.25), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 302 HIS 0.004 0.001 HIS A 824 PHE 0.021 0.002 PHE A 681 TYR 0.039 0.002 TYR A 528 ARG 0.004 0.000 ARG A 478 *********************** 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 172 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 LYS cc_start: 0.5197 (OUTLIER) cc_final: 0.4214 (mmtm) REVERT: A 604 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7180 (tp30) REVERT: B 404 LEU cc_start: 0.7710 (mt) cc_final: 0.7092 (pp) REVERT: B 590 LYS cc_start: 0.5463 (OUTLIER) cc_final: 0.4644 (mmtt) REVERT: B 725 TRP cc_start: 0.6316 (m100) cc_final: 0.5924 (m100) REVERT: B 749 ASP cc_start: 0.6392 (OUTLIER) cc_final: 0.6154 (m-30) REVERT: B 764 PRO cc_start: 0.7005 (Cg_endo) cc_final: 0.6714 (Cg_exo) outliers start: 40 outliers final: 28 residues processed: 166 average time/residue: 0.1799 time to fit residues: 44.4419 Evaluate side-chains 154 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 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 382 PHE Chi-restraints excluded: chain B residue 463 TRP Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 590 LYS 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 845 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 41 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 15 optimal weight: 0.0030 chunk 55 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 58 optimal weight: 20.0000 chunk 93 optimal weight: 0.9980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.5607 r_free = 0.5607 target = 0.281253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5357 r_free = 0.5357 target = 0.250868 restraints weight = 13227.579| |-----------------------------------------------------------------------------| r_work (start): 0.5313 rms_B_bonded: 2.75 r_work: 0.5116 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.5116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5866 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9842 Z= 0.194 Angle : 0.746 10.459 13360 Z= 0.371 Chirality : 0.045 0.201 1480 Planarity : 0.005 0.060 1630 Dihedral : 6.046 36.109 1286 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.76 % Favored : 91.06 % Rotamer: Outliers : 3.47 % Allowed : 24.71 % Favored : 71.81 % Cbeta Deviations : 0.00 % 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: -3.66 (0.22), residues: 1130 helix: -1.72 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -3.47 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 397 HIS 0.004 0.001 HIS B 824 PHE 0.034 0.002 PHE A 851 TYR 0.037 0.002 TYR A 528 ARG 0.003 0.000 ARG B 542 *********************** 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 164 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.7613 (mm-40) cc_final: 0.7350 (mm-40) REVERT: A 590 LYS cc_start: 0.5044 (OUTLIER) cc_final: 0.4116 (mmtm) REVERT: A 604 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7170 (tp30) REVERT: B 404 LEU cc_start: 0.7610 (mt) cc_final: 0.7040 (pp) REVERT: B 524 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7798 (tp) REVERT: B 590 LYS cc_start: 0.5481 (OUTLIER) cc_final: 0.4686 (mmtm) REVERT: B 725 TRP cc_start: 0.6298 (m100) cc_final: 0.5895 (m100) REVERT: B 764 PRO cc_start: 0.7064 (Cg_endo) cc_final: 0.6765 (Cg_exo) REVERT: B 773 MET cc_start: 0.5853 (mmm) cc_final: 0.5621 (mmm) REVERT: B 842 MET cc_start: 0.7808 (mmt) cc_final: 0.7451 (mmt) outliers start: 36 outliers final: 25 residues processed: 157 average time/residue: 0.1739 time to fit residues: 40.9272 Evaluate side-chains 147 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 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 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 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 845 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 70 optimal weight: 0.5980 chunk 21 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 105 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 chunk 108 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 GLN A 608 GLN B 562 ASN ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5588 r_free = 0.5588 target = 0.279695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5343 r_free = 0.5343 target = 0.249598 restraints weight = 12890.885| |-----------------------------------------------------------------------------| r_work (start): 0.5312 rms_B_bonded: 2.68 r_work: 0.5122 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.5122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5864 moved from start: 0.5203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9842 Z= 0.205 Angle : 0.759 12.769 13360 Z= 0.376 Chirality : 0.045 0.180 1480 Planarity : 0.005 0.063 1630 Dihedral : 5.988 34.719 1286 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.65 % Favored : 90.18 % Rotamer: Outliers : 3.47 % Allowed : 24.81 % Favored : 71.72 % Cbeta Deviations : 0.00 % 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: -3.50 (0.23), residues: 1130 helix: -1.58 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -3.40 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 397 HIS 0.003 0.001 HIS A 824 PHE 0.035 0.002 PHE A 851 TYR 0.039 0.002 TYR A 528 ARG 0.007 0.000 ARG B 478 *********************** 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 : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.7527 (mm-40) cc_final: 0.7290 (mm-40) REVERT: A 590 LYS cc_start: 0.5238 (OUTLIER) cc_final: 0.4462 (mmtt) REVERT: A 604 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7174 (tp30) REVERT: B 386 MET cc_start: 0.4710 (mmt) cc_final: 0.4399 (mmt) REVERT: B 404 LEU cc_start: 0.7624 (mt) cc_final: 0.7009 (pp) REVERT: B 553 MET cc_start: 0.6611 (tpt) cc_final: 0.5956 (mmt) REVERT: B 590 LYS cc_start: 0.5604 (OUTLIER) cc_final: 0.4917 (mmtt) REVERT: B 725 TRP cc_start: 0.6236 (m100) cc_final: 0.5862 (m100) REVERT: B 764 PRO cc_start: 0.7071 (Cg_endo) cc_final: 0.6800 (Cg_exo) REVERT: B 773 MET cc_start: 0.5907 (mmm) cc_final: 0.5543 (mmm) REVERT: B 842 MET cc_start: 0.7825 (mmt) cc_final: 0.7579 (mmt) outliers start: 36 outliers final: 27 residues processed: 151 average time/residue: 0.1904 time to fit residues: 42.3014 Evaluate side-chains 146 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 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 382 PHE Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 590 LYS 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 845 ILE Chi-restraints excluded: chain B residue 848 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 106 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 0.2980 chunk 54 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 96 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.5609 r_free = 0.5609 target = 0.281517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5365 r_free = 0.5365 target = 0.251369 restraints weight = 12874.135| |-----------------------------------------------------------------------------| r_work (start): 0.5325 rms_B_bonded: 2.69 r_work: 0.5133 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.5133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5852 moved from start: 0.5350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9842 Z= 0.201 Angle : 0.747 12.158 13360 Z= 0.372 Chirality : 0.046 0.177 1480 Planarity : 0.005 0.065 1630 Dihedral : 5.952 34.242 1286 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 2.70 % Allowed : 25.77 % Favored : 71.53 % Cbeta Deviations : 0.00 % 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: -3.41 (0.23), residues: 1130 helix: -1.51 (0.19), residues: 662 sheet: None (None), residues: 0 loop : -3.36 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 397 HIS 0.003 0.001 HIS A 824 PHE 0.028 0.001 PHE B 851 TYR 0.038 0.002 TYR A 528 ARG 0.008 0.000 ARG B 478 ********************** 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 154 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.7575 (mm-40) cc_final: 0.7333 (mm-40) REVERT: A 386 MET cc_start: 0.4916 (mmt) cc_final: 0.4104 (mmt) REVERT: A 553 MET cc_start: 0.6976 (mmt) cc_final: 0.6286 (mmt) REVERT: A 590 LYS cc_start: 0.5170 (OUTLIER) cc_final: 0.4497 (mmtt) REVERT: A 604 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7175 (tp30) REVERT: A 773 MET cc_start: 0.5346 (mmt) cc_final: 0.4412 (mmt) REVERT: B 386 MET cc_start: 0.4630 (mmt) cc_final: 0.4343 (mmt) REVERT: B 404 LEU cc_start: 0.7646 (mt) cc_final: 0.7051 (pp) REVERT: B 507 MET cc_start: 0.6873 (pmm) cc_final: 0.6649 (pmm) REVERT: B 553 MET cc_start: 0.6626 (tpt) cc_final: 0.5950 (mmt) REVERT: B 590 LYS cc_start: 0.5780 (OUTLIER) cc_final: 0.5132 (mmtt) REVERT: B 725 TRP cc_start: 0.6269 (m100) cc_final: 0.5863 (m100) REVERT: B 764 PRO cc_start: 0.7041 (Cg_endo) cc_final: 0.6763 (Cg_exo) REVERT: B 773 MET cc_start: 0.5995 (mmm) cc_final: 0.5685 (mmm) REVERT: B 842 MET cc_start: 0.7845 (mmt) cc_final: 0.7582 (mmt) outliers start: 28 outliers final: 23 residues processed: 149 average time/residue: 0.1871 time to fit residues: 41.7216 Evaluate side-chains 142 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 382 PHE Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 848 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 11 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 GLN B 559 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 = 0.5588 r_free = 0.5588 target = 0.279114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5327 r_free = 0.5327 target = 0.248425 restraints weight = 12435.397| |-----------------------------------------------------------------------------| r_work (start): 0.5286 rms_B_bonded: 2.69 r_work: 0.5096 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.5096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5896 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9842 Z= 0.220 Angle : 0.773 14.305 13360 Z= 0.382 Chirality : 0.046 0.189 1480 Planarity : 0.005 0.064 1630 Dihedral : 5.964 33.789 1286 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 3.19 % Allowed : 25.48 % 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 (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: -3.35 (0.23), residues: 1130 helix: -1.45 (0.19), residues: 662 sheet: None (None), residues: 0 loop : -3.36 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 397 HIS 0.003 0.001 HIS A 824 PHE 0.030 0.002 PHE B 851 TYR 0.049 0.002 TYR B 828 ARG 0.009 0.000 ARG B 478 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4521.18 seconds wall clock time: 81 minutes 13.42 seconds (4873.42 seconds total)