Starting phenix.real_space_refine on Wed Sep 25 05:18:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p49_20247/09_2024/6p49_20247.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p49_20247/09_2024/6p49_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p49_20247/09_2024/6p49_20247.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p49_20247/09_2024/6p49_20247.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p49_20247/09_2024/6p49_20247.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p49_20247/09_2024/6p49_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-5461/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: 8.94, per 1000 atoms: 0.93 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: 2.41 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.84 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: 2.37 Time building geometry restraints manager: 2.83 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: 0.00 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: 1.130 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.590 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.300 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 34 poor density : 193 time to evaluate : 1.115 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: 0.2434 time to fit residues: 72.5681 Evaluate side-chains 138 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 126 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5707 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 fitting. rotamer outliers: 29 poor density : 155 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 LYS cc_start: 0.4191 (OUTLIER) cc_final: 0.2672 (mmtt) REVERT: A 601 CYS cc_start: 0.5759 (OUTLIER) cc_final: 0.5239 (m) REVERT: B 641 SER cc_start: 0.3551 (OUTLIER) cc_final: 0.3120 (t) REVERT: B 764 PRO cc_start: 0.6367 (Cg_endo) cc_final: 0.6032 (Cg_exo) outliers start: 29 outliers final: 14 residues processed: 176 average time/residue: 0.2090 time to fit residues: 51.5810 Evaluate side-chains 144 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 655 HIS 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 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 58 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 chunk 87 optimal weight: 0.0980 chunk 71 optimal weight: 0.0770 chunk 29 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 104 optimal weight: 0.3980 chunk 35 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5643 moved from start: 0.3415 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= 0.191 Angle : 0.745 15.157 13360 Z= 0.376 Chirality : 0.045 0.214 1480 Planarity : 0.006 0.067 1630 Dihedral : 6.968 40.990 1289 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.50 % Favored : 91.33 % Rotamer: Outliers : 3.09 % Allowed : 18.15 % Favored : 78.76 % 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: -4.83 (0.20), residues: 1130 helix: -2.81 (0.16), residues: 654 sheet: None (None), residues: 0 loop : -3.72 (0.23), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 397 HIS 0.004 0.001 HIS B 129 PHE 0.019 0.002 PHE A 556 TYR 0.029 0.002 TYR A 528 ARG 0.004 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 171 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 139 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 LYS cc_start: 0.4390 (OUTLIER) cc_final: 0.3094 (mmtt) REVERT: B 364 THR cc_start: 0.6473 (OUTLIER) cc_final: 0.6164 (m) outliers start: 32 outliers final: 19 residues processed: 161 average time/residue: 0.1963 time to fit residues: 46.1696 Evaluate side-chains 147 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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 747 THR Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 322 LEU 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 527 ILE Chi-restraints excluded: chain B residue 590 LYS 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 104 optimal weight: 1.9990 chunk 79 optimal weight: 0.0000 chunk 54 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 830 HIS B 94 GLN B 330 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5680 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9842 Z= 0.195 Angle : 0.712 12.438 13360 Z= 0.363 Chirality : 0.045 0.175 1480 Planarity : 0.005 0.062 1630 Dihedral : 6.601 39.736 1288 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.41 % Favored : 91.42 % Rotamer: Outliers : 3.57 % Allowed : 19.98 % Favored : 76.45 % 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: -4.49 (0.20), residues: 1130 helix: -2.48 (0.17), residues: 656 sheet: None (None), residues: 0 loop : -3.66 (0.23), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 397 HIS 0.004 0.001 HIS A 824 PHE 0.019 0.001 PHE A 556 TYR 0.023 0.002 TYR B 776 ARG 0.003 0.000 ARG B 592 *********************** 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 fitting. rotamer outliers: 37 poor density : 137 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 LYS cc_start: 0.4513 (OUTLIER) cc_final: 0.3308 (mmtt) REVERT: B 142 MET cc_start: 0.4210 (tpp) cc_final: 0.3714 (tpp) REVERT: B 404 LEU cc_start: 0.6951 (mt) cc_final: 0.6732 (pp) REVERT: B 524 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7499 (tp) REVERT: B 725 TRP cc_start: 0.6099 (m100) cc_final: 0.5664 (m100) REVERT: B 764 PRO cc_start: 0.6678 (Cg_endo) cc_final: 0.6321 (Cg_exo) outliers start: 37 outliers final: 23 residues processed: 163 average time/residue: 0.1765 time to fit residues: 43.6493 Evaluate side-chains 148 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 123 time to evaluate : 1.138 ------------------------------------------------------------------------------- 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 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 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 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 94 GLN B 559 GLN B 562 ASN ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5690 moved from start: 0.4111 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= 0.201 Angle : 0.723 11.665 13360 Z= 0.365 Chirality : 0.045 0.180 1480 Planarity : 0.005 0.061 1630 Dihedral : 6.420 38.699 1288 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.12 % Favored : 90.71 % Rotamer: Outliers : 3.76 % Allowed : 21.24 % Favored : 75.00 % 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: -4.17 (0.21), residues: 1130 helix: -2.21 (0.18), residues: 660 sheet: None (None), residues: 0 loop : -3.55 (0.24), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 463 HIS 0.003 0.001 HIS A 824 PHE 0.028 0.001 PHE A 681 TYR 0.025 0.002 TYR B 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 168 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 129 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 590 LYS cc_start: 0.4500 (OUTLIER) cc_final: 0.3450 (mmtm) REVERT: B 142 MET cc_start: 0.4421 (tpp) cc_final: 0.3867 (tpp) REVERT: B 590 LYS cc_start: 0.5369 (OUTLIER) cc_final: 0.4277 (mmtm) REVERT: B 725 TRP cc_start: 0.6158 (m100) cc_final: 0.5794 (m100) REVERT: B 750 MET cc_start: 0.6436 (tpt) cc_final: 0.6232 (tpt) outliers start: 39 outliers final: 26 residues processed: 160 average time/residue: 0.1815 time to fit residues: 44.4190 Evaluate side-chains 150 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 122 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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 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 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 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 535 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 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 37 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 27 optimal weight: 0.1980 chunk 112 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 58 optimal weight: 20.0000 chunk 108 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 620 ASN A 710 GLN A 726 GLN ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 GLN B 844 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5671 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9842 Z= 0.188 Angle : 0.708 10.949 13360 Z= 0.357 Chirality : 0.045 0.197 1480 Planarity : 0.005 0.062 1630 Dihedral : 6.145 37.434 1287 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.32 % Favored : 91.50 % Rotamer: Outliers : 2.99 % Allowed : 23.26 % 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: -3.87 (0.22), residues: 1130 helix: -1.92 (0.18), residues: 650 sheet: None (None), residues: 0 loop : -3.50 (0.24), residues: 480 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 0.025 0.001 PHE B 374 TYR 0.023 0.001 TYR B 776 ARG 0.004 0.000 ARG B 542 *********************** 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 158 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 524 LEU cc_start: 0.7243 (tt) cc_final: 0.6418 (tt) REVERT: A 562 ASN cc_start: 0.6986 (m-40) cc_final: 0.6157 (m-40) REVERT: A 590 LYS cc_start: 0.4877 (OUTLIER) cc_final: 0.3934 (mmtm) REVERT: B 590 LYS cc_start: 0.5294 (OUTLIER) cc_final: 0.4391 (mmtm) REVERT: B 725 TRP cc_start: 0.6097 (m100) cc_final: 0.5767 (m100) REVERT: B 764 PRO cc_start: 0.6543 (Cg_endo) cc_final: 0.6180 (Cg_exo) outliers start: 31 outliers final: 24 residues processed: 150 average time/residue: 0.1688 time to fit residues: 38.6565 Evaluate side-chains 146 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 120 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 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 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 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 590 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.2980 chunk 63 optimal weight: 0.1980 chunk 81 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 A 844 HIS ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5668 moved from start: 0.4726 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= 0.189 Angle : 0.720 10.753 13360 Z= 0.359 Chirality : 0.045 0.241 1480 Planarity : 0.005 0.064 1630 Dihedral : 6.066 36.454 1287 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.29 % Favored : 90.53 % Rotamer: Outliers : 3.38 % Allowed : 23.75 % Favored : 72.88 % 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: -3.72 (0.22), residues: 1130 helix: -1.78 (0.18), residues: 658 sheet: None (None), residues: 0 loop : -3.45 (0.25), residues: 472 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 0.024 0.001 PHE A 681 TYR 0.023 0.001 TYR B 776 ARG 0.004 0.000 ARG B 808 *********************** 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 166 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 131 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6459 (mm110) cc_final: 0.6225 (mm-40) REVERT: A 524 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7529 (tt) REVERT: A 562 ASN cc_start: 0.6780 (m-40) cc_final: 0.5831 (m-40) REVERT: A 590 LYS cc_start: 0.5040 (OUTLIER) cc_final: 0.4120 (mmtm) REVERT: B 404 LEU cc_start: 0.7104 (mt) cc_final: 0.6687 (pp) REVERT: B 590 LYS cc_start: 0.5373 (OUTLIER) cc_final: 0.4552 (mmtm) REVERT: B 725 TRP cc_start: 0.6078 (m100) cc_final: 0.5751 (m100) REVERT: B 764 PRO cc_start: 0.6492 (Cg_endo) cc_final: 0.6134 (Cg_exo) REVERT: B 842 MET cc_start: 0.7206 (mmt) cc_final: 0.6796 (mmt) outliers start: 35 outliers final: 23 residues processed: 159 average time/residue: 0.1744 time to fit residues: 41.3541 Evaluate side-chains 146 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 120 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 524 LEU 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 654 TYR Chi-restraints excluded: chain A residue 671 MET 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 76 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 ASN A 608 GLN ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5696 moved from start: 0.4957 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= 0.200 Angle : 0.739 10.540 13360 Z= 0.368 Chirality : 0.045 0.212 1480 Planarity : 0.005 0.064 1630 Dihedral : 6.003 36.472 1286 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.20 % Favored : 90.62 % Rotamer: Outliers : 3.09 % Allowed : 24.13 % Favored : 72.78 % 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: -3.61 (0.22), residues: 1130 helix: -1.70 (0.19), residues: 662 sheet: None (None), residues: 0 loop : -3.41 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 397 HIS 0.005 0.001 HIS A 844 PHE 0.022 0.002 PHE A 681 TYR 0.030 0.002 TYR B 847 ARG 0.003 0.000 ARG A 753 *********************** 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 159 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 127 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 MET cc_start: 0.4995 (mmt) cc_final: 0.4345 (mmt) REVERT: A 590 LYS cc_start: 0.5113 (OUTLIER) cc_final: 0.4124 (mmtm) REVERT: B 404 LEU cc_start: 0.7030 (mt) cc_final: 0.6653 (pp) REVERT: B 590 LYS cc_start: 0.5342 (OUTLIER) cc_final: 0.4651 (mmtm) REVERT: B 725 TRP cc_start: 0.6196 (m100) cc_final: 0.5841 (m100) REVERT: B 750 MET cc_start: 0.6331 (tpt) cc_final: 0.6079 (tpt) REVERT: B 764 PRO cc_start: 0.6576 (Cg_endo) cc_final: 0.6230 (Cg_exo) REVERT: B 842 MET cc_start: 0.7300 (mmt) cc_final: 0.6962 (mmt) outliers start: 32 outliers final: 24 residues processed: 153 average time/residue: 0.1681 time to fit residues: 38.8254 Evaluate side-chains 147 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 121 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 611 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 671 MET 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 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 732 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 847 TYR 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 107 optimal weight: 2.9990 chunk 62 optimal weight: 0.2980 chunk 45 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 110 optimal weight: 0.1980 chunk 67 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 ASN A 608 GLN B 559 GLN ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5727 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 9842 Z= 0.229 Angle : 0.772 16.066 13360 Z= 0.380 Chirality : 0.046 0.221 1480 Planarity : 0.005 0.062 1630 Dihedral : 6.014 35.661 1286 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.82 % Favored : 90.00 % Rotamer: Outliers : 2.99 % Allowed : 24.81 % Favored : 72.20 % 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: -3.45 (0.23), residues: 1130 helix: -1.55 (0.19), residues: 644 sheet: None (None), residues: 0 loop : -3.33 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 397 HIS 0.004 0.001 HIS A 824 PHE 0.040 0.002 PHE B 851 TYR 0.027 0.002 TYR B 828 ARG 0.003 0.000 ARG A 753 *********************** 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 157 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 126 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6297 (mm-40) cc_final: 0.6050 (mm-40) REVERT: A 386 MET cc_start: 0.5032 (mmt) cc_final: 0.4392 (mmt) REVERT: A 590 LYS cc_start: 0.5207 (OUTLIER) cc_final: 0.4405 (mmtt) REVERT: B 142 MET cc_start: 0.4767 (tpp) cc_final: 0.4253 (tpp) REVERT: B 404 LEU cc_start: 0.7076 (mt) cc_final: 0.6652 (pp) REVERT: B 590 LYS cc_start: 0.5393 (OUTLIER) cc_final: 0.4727 (mmtm) REVERT: B 750 MET cc_start: 0.6402 (tpt) cc_final: 0.6102 (tpt) REVERT: B 764 PRO cc_start: 0.6675 (Cg_endo) cc_final: 0.6357 (Cg_exo) REVERT: B 842 MET cc_start: 0.7347 (mmt) cc_final: 0.6936 (mmt) outliers start: 31 outliers final: 24 residues processed: 153 average time/residue: 0.1701 time to fit residues: 39.1687 Evaluate side-chains 147 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 121 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 611 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 671 MET 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 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 732 ILE Chi-restraints excluded: chain B residue 747 THR 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 52 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 92 optimal weight: 0.0370 chunk 9 optimal weight: 0.3980 chunk 71 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 73 optimal weight: 0.4980 chunk 98 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5664 moved from start: 0.5359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9842 Z= 0.192 Angle : 0.745 17.757 13360 Z= 0.367 Chirality : 0.046 0.265 1480 Planarity : 0.005 0.065 1630 Dihedral : 5.866 34.389 1286 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 2.80 % Allowed : 25.19 % 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 (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: -3.28 (0.23), residues: 1130 helix: -1.38 (0.19), residues: 656 sheet: None (None), residues: 0 loop : -3.33 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 397 HIS 0.003 0.001 HIS B 844 PHE 0.039 0.001 PHE B 851 TYR 0.029 0.001 TYR A 306 ARG 0.002 0.000 ARG A 753 ********************** 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 157 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 128 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6227 (mm-40) cc_final: 0.5994 (mm-40) REVERT: A 386 MET cc_start: 0.4865 (mmt) cc_final: 0.4269 (mmt) REVERT: A 553 MET cc_start: 0.6357 (mmt) cc_final: 0.5956 (mmt) REVERT: A 590 LYS cc_start: 0.5303 (OUTLIER) cc_final: 0.4607 (mmtt) REVERT: B 142 MET cc_start: 0.4568 (tpp) cc_final: 0.4049 (tpp) REVERT: B 404 LEU cc_start: 0.7013 (mt) cc_final: 0.6604 (pp) REVERT: B 590 LYS cc_start: 0.5748 (OUTLIER) cc_final: 0.5129 (mmtm) REVERT: B 750 MET cc_start: 0.6413 (tpt) cc_final: 0.6155 (tpt) REVERT: B 764 PRO cc_start: 0.6582 (Cg_endo) cc_final: 0.6254 (Cg_exo) REVERT: B 842 MET cc_start: 0.7242 (mmt) cc_final: 0.6923 (mmt) outliers start: 29 outliers final: 25 residues processed: 152 average time/residue: 0.1646 time to fit residues: 37.9709 Evaluate side-chains 146 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 611 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 671 MET 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 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 732 ILE Chi-restraints excluded: chain B residue 747 THR 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 84 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 92 optimal weight: 0.0270 chunk 38 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 ASN ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5607 r_free = 0.5607 target = 0.281718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5352 r_free = 0.5352 target = 0.251394 restraints weight = 12335.687| |-----------------------------------------------------------------------------| r_work (start): 0.5318 rms_B_bonded: 2.75 r_work: 0.5121 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.5121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5842 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9842 Z= 0.200 Angle : 0.765 14.378 13360 Z= 0.373 Chirality : 0.046 0.241 1480 Planarity : 0.005 0.066 1630 Dihedral : 5.817 33.827 1286 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 2.51 % Allowed : 25.77 % 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: -3.14 (0.23), residues: 1130 helix: -1.25 (0.19), residues: 644 sheet: None (None), residues: 0 loop : -3.26 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 650 HIS 0.003 0.001 HIS B 844 PHE 0.027 0.002 PHE A 851 TYR 0.035 0.002 TYR A 822 ARG 0.002 0.000 ARG A 753 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2118.58 seconds wall clock time: 39 minutes 6.34 seconds (2346.34 seconds total)