Starting phenix.real_space_refine on Wed Sep 25 11:27:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh3_23335/09_2024/7lh3_23335.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh3_23335/09_2024/7lh3_23335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh3_23335/09_2024/7lh3_23335.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh3_23335/09_2024/7lh3_23335.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh3_23335/09_2024/7lh3_23335.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh3_23335/09_2024/7lh3_23335.cif" } resolution = 4.3 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= 0.007 sd= 0.020 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6862 2.51 5 N 1690 2.21 5 O 1852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10452 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5226 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 34, 'TRANS': 645} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Restraints were copied for chains: B Time building chain proxies: 10.33, per 1000 atoms: 0.99 Number of scatterers: 10452 At special positions: 0 Unit cell: (102.16, 119.078, 113.222, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1852 8.00 N 1690 7.00 C 6862 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.90 Conformation dependent library (CDL) restraints added in 1.2 seconds 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2512 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 5 sheets defined 71.5% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 24 through 31 Processing helix chain 'A' and resid 41 through 48 removed outlier: 4.243A pdb=" N GLN A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 75 through 105 removed outlier: 5.182A pdb=" N LEU A 81 " --> pdb=" O LYS A 77 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLY A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) Proline residue: A 96 - end of helix Processing helix chain 'A' and resid 108 through 115 removed outlier: 3.988A pdb=" N GLY A 112 " --> pdb=" O PRO A 108 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 127 removed outlier: 3.715A pdb=" N PHE A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 152 Processing helix chain 'A' and resid 168 through 196 Processing helix chain 'A' and resid 197 through 205 removed outlier: 4.087A pdb=" N PHE A 200 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 203 " --> pdb=" O PHE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 225 Processing helix chain 'A' and resid 225 through 231 Processing helix chain 'A' and resid 241 through 253 Processing helix chain 'A' and resid 254 through 257 Processing helix chain 'A' and resid 258 through 282 Processing helix chain 'A' and resid 291 through 308 removed outlier: 3.543A pdb=" N PHE A 295 " --> pdb=" O PRO A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 removed outlier: 3.744A pdb=" N TYR A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 366 removed outlier: 6.430A pdb=" N VAL A 341 " --> pdb=" O HIS A 337 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ASP A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 388 Processing helix chain 'A' and resid 396 through 406 Processing helix chain 'A' and resid 411 through 428 removed outlier: 3.513A pdb=" N CYS A 415 " --> pdb=" O GLN A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 removed outlier: 4.188A pdb=" N SER A 434 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 448 removed outlier: 3.847A pdb=" N LEU A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 456 through 465 removed outlier: 3.875A pdb=" N PHE A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 481 Processing helix chain 'A' and resid 483 through 505 removed outlier: 3.713A pdb=" N LEU A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ILE A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 560 removed outlier: 3.605A pdb=" N THR A 560 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 579 Processing helix chain 'A' and resid 626 through 631 Processing helix chain 'A' and resid 653 through 670 removed outlier: 3.626A pdb=" N VAL A 670 " --> pdb=" O GLU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 690 Processing helix chain 'A' and resid 691 through 694 removed outlier: 3.737A pdb=" N GLU A 694 " --> pdb=" O ARG A 691 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 691 through 694' Processing helix chain 'A' and resid 695 through 702 removed outlier: 3.942A pdb=" N GLU A 700 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 702 " --> pdb=" O TRP A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 723 removed outlier: 3.591A pdb=" N GLU A 723 " --> pdb=" O LEU A 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 31 Processing helix chain 'B' and resid 41 through 48 removed outlier: 4.243A pdb=" N GLN B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 53 through 65 Processing helix chain 'B' and resid 66 through 71 Processing helix chain 'B' and resid 75 through 105 removed outlier: 5.182A pdb=" N LEU B 81 " --> pdb=" O LYS B 77 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLY B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Proline residue: B 96 - end of helix Processing helix chain 'B' and resid 108 through 115 removed outlier: 3.987A pdb=" N GLY B 112 " --> pdb=" O PRO B 108 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 113 " --> pdb=" O PRO B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 127 removed outlier: 3.715A pdb=" N PHE B 125 " --> pdb=" O ILE B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 152 Processing helix chain 'B' and resid 168 through 196 Processing helix chain 'B' and resid 197 through 205 removed outlier: 4.086A pdb=" N PHE B 200 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 203 " --> pdb=" O PHE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 225 Processing helix chain 'B' and resid 225 through 231 Processing helix chain 'B' and resid 241 through 253 Processing helix chain 'B' and resid 254 through 257 Processing helix chain 'B' and resid 258 through 282 Processing helix chain 'B' and resid 291 through 308 removed outlier: 3.543A pdb=" N PHE B 295 " --> pdb=" O PRO B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.744A pdb=" N TYR B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 366 removed outlier: 6.430A pdb=" N VAL B 341 " --> pdb=" O HIS B 337 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ASP B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 396 through 406 Processing helix chain 'B' and resid 411 through 428 removed outlier: 3.513A pdb=" N CYS B 415 " --> pdb=" O GLN B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 removed outlier: 4.189A pdb=" N SER B 434 " --> pdb=" O LEU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 448 removed outlier: 3.847A pdb=" N LEU B 440 " --> pdb=" O PRO B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 456 through 465 removed outlier: 3.875A pdb=" N PHE B 460 " --> pdb=" O SER B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 481 Processing helix chain 'B' and resid 483 through 505 removed outlier: 3.713A pdb=" N LEU B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ILE B 489 " --> pdb=" O ASP B 485 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 560 removed outlier: 3.605A pdb=" N THR B 560 " --> pdb=" O LEU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 579 Processing helix chain 'B' and resid 626 through 631 Processing helix chain 'B' and resid 653 through 670 removed outlier: 3.627A pdb=" N VAL B 670 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 690 Processing helix chain 'B' and resid 691 through 694 removed outlier: 3.737A pdb=" N GLU B 694 " --> pdb=" O ARG B 691 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 691 through 694' Processing helix chain 'B' and resid 695 through 702 removed outlier: 3.943A pdb=" N GLU B 700 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 702 " --> pdb=" O TRP B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 723 removed outlier: 3.590A pdb=" N GLU B 723 " --> pdb=" O LEU B 719 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 20 removed outlier: 3.817A pdb=" N VAL A 18 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL B 18 " --> pdb=" O VAL A 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 135 removed outlier: 3.607A pdb=" N GLY A 135 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 394 " --> pdb=" O GLY A 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 522 removed outlier: 3.520A pdb=" N LYS A 509 " --> pdb=" O GLN A 539 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 511 " --> pdb=" O ILE A 537 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ILE A 537 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N LYS A 513 " --> pdb=" O ILE A 535 " (cutoff:3.500A) removed outlier: 11.976A pdb=" N ILE A 535 " --> pdb=" O LYS A 513 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LYS A 536 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ASP A 645 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N PHE A 538 " --> pdb=" O ASP A 645 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 134 through 135 removed outlier: 3.606A pdb=" N GLY B 135 " --> pdb=" O SER B 394 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER B 394 " --> pdb=" O GLY B 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 520 through 522 removed outlier: 3.520A pdb=" N LYS B 509 " --> pdb=" O GLN B 539 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 511 " --> pdb=" O ILE B 537 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ILE B 537 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N LYS B 513 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 11.976A pdb=" N ILE B 535 " --> pdb=" O LYS B 513 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LYS B 536 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ASP B 645 " --> pdb=" O LYS B 536 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N PHE B 538 " --> pdb=" O ASP B 645 " (cutoff:3.500A) 656 hydrogen bonds defined for protein. 1902 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: 3.41 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3236 1.34 - 1.46: 2311 1.46 - 1.58: 5063 1.58 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 10688 Sorted by residual: bond pdb=" CA ILE A 532 " pdb=" CB ILE A 532 " ideal model delta sigma weight residual 1.537 1.529 0.008 1.29e-02 6.01e+03 4.04e-01 bond pdb=" C LEU B 71 " pdb=" N PRO B 72 " ideal model delta sigma weight residual 1.335 1.342 -0.007 1.28e-02 6.10e+03 3.41e-01 bond pdb=" C GLY A 408 " pdb=" O GLY A 408 " ideal model delta sigma weight residual 1.235 1.243 -0.008 1.35e-02 5.49e+03 3.41e-01 bond pdb=" C GLY B 408 " pdb=" O GLY B 408 " ideal model delta sigma weight residual 1.235 1.243 -0.008 1.35e-02 5.49e+03 3.36e-01 bond pdb=" N PRO B 327 " pdb=" CA PRO B 327 " ideal model delta sigma weight residual 1.459 1.467 -0.008 1.40e-02 5.10e+03 3.20e-01 ... (remaining 10683 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 14199 1.03 - 2.07: 245 2.07 - 3.10: 70 3.10 - 4.14: 6 4.14 - 5.17: 12 Bond angle restraints: 14532 Sorted by residual: angle pdb=" N THR A 517 " pdb=" CA THR A 517 " pdb=" C THR A 517 " ideal model delta sigma weight residual 108.34 110.93 -2.59 1.31e+00 5.83e-01 3.90e+00 angle pdb=" N THR B 517 " pdb=" CA THR B 517 " pdb=" C THR B 517 " ideal model delta sigma weight residual 108.34 110.90 -2.56 1.31e+00 5.83e-01 3.81e+00 angle pdb=" N SER A 24 " pdb=" CA SER A 24 " pdb=" C SER A 24 " ideal model delta sigma weight residual 110.53 108.23 2.30 1.29e+00 6.01e-01 3.18e+00 angle pdb=" N SER B 24 " pdb=" CA SER B 24 " pdb=" C SER B 24 " ideal model delta sigma weight residual 110.53 108.26 2.27 1.29e+00 6.01e-01 3.09e+00 angle pdb=" NE ARG A 31 " pdb=" CZ ARG A 31 " pdb=" NH1 ARG A 31 " ideal model delta sigma weight residual 121.50 120.00 1.50 1.00e+00 1.00e+00 2.26e+00 ... (remaining 14527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.64: 6013 12.64 - 25.27: 243 25.27 - 37.91: 68 37.91 - 50.55: 8 50.55 - 63.18: 6 Dihedral angle restraints: 6338 sinusoidal: 2414 harmonic: 3924 Sorted by residual: dihedral pdb=" CA LEU B 184 " pdb=" CB LEU B 184 " pdb=" CG LEU B 184 " pdb=" CD1 LEU B 184 " ideal model delta sinusoidal sigma weight residual 60.00 118.45 -58.45 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LEU A 184 " pdb=" CB LEU A 184 " pdb=" CG LEU A 184 " pdb=" CD1 LEU A 184 " ideal model delta sinusoidal sigma weight residual 60.00 118.44 -58.44 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LEU B 422 " pdb=" CB LEU B 422 " pdb=" CG LEU B 422 " pdb=" CD1 LEU B 422 " ideal model delta sinusoidal sigma weight residual 180.00 123.35 56.65 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 6335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 996 0.025 - 0.050: 406 0.050 - 0.075: 210 0.075 - 0.100: 73 0.100 - 0.126: 43 Chirality restraints: 1728 Sorted by residual: chirality pdb=" CA ILE A 532 " pdb=" N ILE A 532 " pdb=" C ILE A 532 " pdb=" CB ILE A 532 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA ILE B 532 " pdb=" N ILE B 532 " pdb=" C ILE B 532 " pdb=" CB ILE B 532 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA ILE B 290 " pdb=" N ILE B 290 " pdb=" C ILE B 290 " pdb=" CB ILE B 290 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 1725 not shown) Planarity restraints: 1808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 542 " -0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO A 543 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 543 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 543 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 542 " 0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO B 543 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 543 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 543 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 53 " -0.018 5.00e-02 4.00e+02 2.69e-02 1.15e+00 pdb=" N PRO B 54 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO B 54 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 54 " -0.015 5.00e-02 4.00e+02 ... (remaining 1805 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2359 2.79 - 3.31: 10623 3.31 - 3.84: 17205 3.84 - 4.37: 18938 4.37 - 4.90: 33623 Nonbonded interactions: 82748 Sorted by model distance: nonbonded pdb=" O ALA B 495 " pdb=" OG1 THR B 498 " model vdw 2.258 3.040 nonbonded pdb=" O ALA A 495 " pdb=" OG1 THR A 498 " model vdw 2.258 3.040 nonbonded pdb=" OD2 ASP A 83 " pdb=" OG1 THR A 410 " model vdw 2.316 3.040 nonbonded pdb=" O LEU B 556 " pdb=" OG1 THR B 560 " model vdw 2.316 3.040 nonbonded pdb=" O LEU A 556 " pdb=" OG1 THR A 560 " model vdw 2.317 3.040 ... (remaining 82743 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 group one per residue 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: 0.870 Set stop_for_unknowns flag: 0.010 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: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 31.100 Find NCS groups from input model: 0.280 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 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 : 0.001 0.014 10688 Z= 0.090 Angle : 0.399 5.170 14532 Z= 0.224 Chirality : 0.039 0.126 1728 Planarity : 0.003 0.029 1808 Dihedral : 7.882 63.182 3826 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.06 % Allowed : 4.94 % Favored : 94.00 % 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: 2.29 (0.25), residues: 1352 helix: 2.34 (0.19), residues: 908 sheet: 3.14 (0.70), residues: 52 loop : -0.75 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 70 HIS 0.002 0.000 HIS B 25 PHE 0.005 0.001 PHE B 269 TYR 0.008 0.001 TYR A 340 ARG 0.001 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 302 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 MET cc_start: 0.7309 (tpt) cc_final: 0.7014 (tpp) REVERT: A 633 MET cc_start: 0.7954 (tpt) cc_final: 0.7561 (tpp) REVERT: A 669 ASP cc_start: 0.7836 (t0) cc_final: 0.7532 (t0) REVERT: B 357 MET cc_start: 0.7373 (tpt) cc_final: 0.7051 (tpp) REVERT: B 482 LEU cc_start: 0.9013 (mt) cc_final: 0.8790 (tt) REVERT: B 633 MET cc_start: 0.8036 (tpt) cc_final: 0.7537 (tpp) REVERT: B 669 ASP cc_start: 0.7739 (t0) cc_final: 0.7502 (t0) REVERT: B 719 LEU cc_start: 0.9397 (mt) cc_final: 0.9189 (mm) outliers start: 12 outliers final: 0 residues processed: 306 average time/residue: 0.2336 time to fit residues: 97.7524 Evaluate side-chains 144 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 7.9990 chunk 103 optimal weight: 40.0000 chunk 57 optimal weight: 0.0970 chunk 35 optimal weight: 30.0000 chunk 69 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 106 optimal weight: 50.0000 chunk 41 optimal weight: 0.0030 chunk 64 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 chunk 123 optimal weight: 0.4980 overall best weight: 1.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 722 GLN B 447 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10688 Z= 0.143 Angle : 0.524 7.822 14532 Z= 0.261 Chirality : 0.042 0.148 1728 Planarity : 0.004 0.031 1808 Dihedral : 2.932 12.593 1456 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % 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: 2.23 (0.24), residues: 1352 helix: 2.19 (0.18), residues: 906 sheet: 3.37 (0.72), residues: 52 loop : -0.52 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 70 HIS 0.002 0.001 HIS A 25 PHE 0.010 0.001 PHE A 452 TYR 0.016 0.001 TYR A 123 ARG 0.003 0.000 ARG A 571 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ILE cc_start: 0.8307 (pt) cc_final: 0.8073 (pt) REVERT: A 180 MET cc_start: 0.8530 (tpp) cc_final: 0.7921 (mmm) REVERT: A 357 MET cc_start: 0.7381 (tpt) cc_final: 0.7018 (tpp) REVERT: A 633 MET cc_start: 0.8004 (tpt) cc_final: 0.7626 (tpp) REVERT: B 63 MET cc_start: 0.8748 (ptp) cc_final: 0.8296 (ptm) REVERT: B 180 MET cc_start: 0.8620 (tpp) cc_final: 0.8108 (mmm) REVERT: B 299 MET cc_start: 0.8225 (mmp) cc_final: 0.7770 (tmm) REVERT: B 357 MET cc_start: 0.7408 (tpt) cc_final: 0.6999 (tpp) REVERT: B 482 LEU cc_start: 0.9036 (mt) cc_final: 0.8785 (tt) REVERT: B 633 MET cc_start: 0.8195 (tpt) cc_final: 0.7649 (tpp) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2084 time to fit residues: 54.6375 Evaluate side-chains 135 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 10.0000 chunk 38 optimal weight: 30.0000 chunk 102 optimal weight: 6.9990 chunk 84 optimal weight: 50.0000 chunk 34 optimal weight: 5.9990 chunk 123 optimal weight: 40.0000 chunk 133 optimal weight: 6.9990 chunk 110 optimal weight: 20.0000 chunk 122 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10688 Z= 0.226 Angle : 0.545 6.536 14532 Z= 0.276 Chirality : 0.043 0.138 1728 Planarity : 0.004 0.031 1808 Dihedral : 3.213 14.272 1456 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.26 % Allowed : 2.12 % Favored : 97.62 % 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: 2.10 (0.24), residues: 1352 helix: 2.14 (0.18), residues: 906 sheet: 2.79 (0.74), residues: 52 loop : -0.60 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 699 HIS 0.005 0.001 HIS A 25 PHE 0.011 0.001 PHE A 703 TYR 0.012 0.001 TYR A 123 ARG 0.010 0.001 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 172 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ILE cc_start: 0.8442 (pt) cc_final: 0.8193 (pt) REVERT: A 180 MET cc_start: 0.8558 (tpp) cc_final: 0.7998 (mmm) REVERT: A 196 CYS cc_start: 0.8471 (p) cc_final: 0.8267 (p) REVERT: A 299 MET cc_start: 0.8219 (mmp) cc_final: 0.7693 (tmm) REVERT: A 357 MET cc_start: 0.7466 (tpt) cc_final: 0.7189 (tpp) REVERT: A 435 LEU cc_start: 0.8745 (mm) cc_final: 0.8475 (mm) REVERT: A 633 MET cc_start: 0.8271 (tpt) cc_final: 0.7806 (tpp) REVERT: A 665 LYS cc_start: 0.8863 (tptp) cc_final: 0.8517 (tppt) REVERT: B 121 ILE cc_start: 0.9194 (pt) cc_final: 0.8931 (mm) REVERT: B 180 MET cc_start: 0.8703 (tpp) cc_final: 0.8163 (mmm) REVERT: B 299 MET cc_start: 0.8317 (mmp) cc_final: 0.7826 (tmm) REVERT: B 357 MET cc_start: 0.7475 (tpt) cc_final: 0.7192 (tpp) REVERT: B 435 LEU cc_start: 0.8763 (mm) cc_final: 0.8478 (mm) REVERT: B 451 MET cc_start: 0.7447 (tpp) cc_final: 0.7165 (tpp) REVERT: B 482 LEU cc_start: 0.9037 (mt) cc_final: 0.8802 (tt) REVERT: B 633 MET cc_start: 0.8415 (tpt) cc_final: 0.7808 (tpp) REVERT: B 665 LYS cc_start: 0.8991 (tptp) cc_final: 0.8678 (tppt) outliers start: 3 outliers final: 2 residues processed: 175 average time/residue: 0.2076 time to fit residues: 53.6181 Evaluate side-chains 129 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 64 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 chunk 59 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 30.0000 chunk 131 optimal weight: 10.0000 chunk 117 optimal weight: 0.9990 chunk 35 optimal weight: 20.0000 chunk 109 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 454 GLN B 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10688 Z= 0.188 Angle : 0.522 6.311 14532 Z= 0.263 Chirality : 0.043 0.139 1728 Planarity : 0.004 0.039 1808 Dihedral : 3.318 14.865 1456 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % 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: 2.02 (0.24), residues: 1352 helix: 2.03 (0.18), residues: 910 sheet: 2.51 (0.74), residues: 52 loop : -0.47 (0.34), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 70 HIS 0.005 0.001 HIS B 25 PHE 0.015 0.001 PHE A 452 TYR 0.014 0.001 TYR B 552 ARG 0.006 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ILE cc_start: 0.8465 (pt) cc_final: 0.8142 (pt) REVERT: A 180 MET cc_start: 0.8621 (tpp) cc_final: 0.7973 (mmm) REVERT: A 196 CYS cc_start: 0.8445 (p) cc_final: 0.8238 (p) REVERT: A 299 MET cc_start: 0.8232 (mmp) cc_final: 0.7730 (tmm) REVERT: A 357 MET cc_start: 0.7451 (tpt) cc_final: 0.7147 (tpp) REVERT: A 435 LEU cc_start: 0.8778 (mm) cc_final: 0.8571 (mm) REVERT: A 452 PHE cc_start: 0.8435 (m-10) cc_final: 0.8088 (t80) REVERT: A 488 LEU cc_start: 0.8981 (tt) cc_final: 0.8638 (tp) REVERT: A 633 MET cc_start: 0.8283 (tpt) cc_final: 0.7813 (tpp) REVERT: A 665 LYS cc_start: 0.8923 (tptp) cc_final: 0.8539 (tppt) REVERT: B 121 ILE cc_start: 0.9200 (pt) cc_final: 0.8939 (mm) REVERT: B 180 MET cc_start: 0.8694 (tpp) cc_final: 0.8132 (mmm) REVERT: B 196 CYS cc_start: 0.8579 (p) cc_final: 0.8374 (p) REVERT: B 299 MET cc_start: 0.8338 (mmp) cc_final: 0.7863 (tmm) REVERT: B 357 MET cc_start: 0.7574 (tpt) cc_final: 0.7236 (tpp) REVERT: B 435 LEU cc_start: 0.8772 (mm) cc_final: 0.8572 (mm) REVERT: B 482 LEU cc_start: 0.9066 (mt) cc_final: 0.8817 (tt) REVERT: B 497 LEU cc_start: 0.8948 (mt) cc_final: 0.8748 (tt) REVERT: B 633 MET cc_start: 0.8426 (tpt) cc_final: 0.7798 (tpp) REVERT: B 665 LYS cc_start: 0.9003 (tptp) cc_final: 0.8637 (tppt) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1915 time to fit residues: 47.6256 Evaluate side-chains 129 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 112 optimal weight: 7.9990 chunk 90 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 67 optimal weight: 3.9990 chunk 117 optimal weight: 0.0980 chunk 33 optimal weight: 20.0000 chunk 44 optimal weight: 9.9990 overall best weight: 5.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10688 Z= 0.202 Angle : 0.547 7.208 14532 Z= 0.275 Chirality : 0.043 0.145 1728 Planarity : 0.004 0.040 1808 Dihedral : 3.475 18.161 1456 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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: 2.00 (0.24), residues: 1352 helix: 1.98 (0.18), residues: 910 sheet: 3.13 (0.89), residues: 38 loop : -0.33 (0.34), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 70 HIS 0.006 0.001 HIS A 25 PHE 0.010 0.001 PHE A 198 TYR 0.029 0.002 TYR A 79 ARG 0.004 0.000 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ILE cc_start: 0.8442 (pt) cc_final: 0.8177 (pt) REVERT: A 180 MET cc_start: 0.8635 (tpp) cc_final: 0.8039 (mmm) REVERT: A 299 MET cc_start: 0.8249 (mmp) cc_final: 0.7754 (tmm) REVERT: A 357 MET cc_start: 0.7512 (tpt) cc_final: 0.7208 (tpp) REVERT: A 435 LEU cc_start: 0.8764 (mm) cc_final: 0.8519 (mm) REVERT: A 452 PHE cc_start: 0.8603 (m-10) cc_final: 0.8051 (m-80) REVERT: A 488 LEU cc_start: 0.9039 (tt) cc_final: 0.8704 (tp) REVERT: A 509 LYS cc_start: 0.8654 (mttt) cc_final: 0.8308 (mmmt) REVERT: A 633 MET cc_start: 0.8319 (tpt) cc_final: 0.7810 (tpp) REVERT: A 665 LYS cc_start: 0.8969 (tptp) cc_final: 0.8572 (tppt) REVERT: A 669 ASP cc_start: 0.7748 (m-30) cc_final: 0.7505 (m-30) REVERT: B 121 ILE cc_start: 0.9220 (pt) cc_final: 0.8971 (mm) REVERT: B 132 ILE cc_start: 0.8727 (pt) cc_final: 0.8517 (pt) REVERT: B 180 MET cc_start: 0.8707 (tpp) cc_final: 0.8182 (mmm) REVERT: B 196 CYS cc_start: 0.8585 (p) cc_final: 0.8378 (p) REVERT: B 299 MET cc_start: 0.8335 (mmp) cc_final: 0.7870 (tmm) REVERT: B 357 MET cc_start: 0.7490 (tpt) cc_final: 0.7151 (tpp) REVERT: B 435 LEU cc_start: 0.8731 (mm) cc_final: 0.8486 (mm) REVERT: B 452 PHE cc_start: 0.8406 (m-10) cc_final: 0.7938 (m-80) REVERT: B 482 LEU cc_start: 0.9078 (mt) cc_final: 0.8826 (tt) REVERT: B 633 MET cc_start: 0.8459 (tpt) cc_final: 0.7848 (tpp) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2071 time to fit residues: 51.0102 Evaluate side-chains 126 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 6.9990 chunk 25 optimal weight: 30.0000 chunk 77 optimal weight: 20.0000 chunk 32 optimal weight: 8.9990 chunk 131 optimal weight: 20.0000 chunk 109 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 GLN B 648 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10688 Z= 0.242 Angle : 0.582 6.728 14532 Z= 0.292 Chirality : 0.044 0.172 1728 Planarity : 0.004 0.036 1808 Dihedral : 3.627 18.385 1456 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.91 (0.24), residues: 1352 helix: 1.92 (0.18), residues: 910 sheet: 2.90 (0.89), residues: 38 loop : -0.36 (0.34), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 699 HIS 0.008 0.001 HIS A 25 PHE 0.044 0.002 PHE A 230 TYR 0.021 0.002 TYR A 552 ARG 0.002 0.000 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ILE cc_start: 0.8493 (pt) cc_final: 0.8172 (pt) REVERT: A 299 MET cc_start: 0.8297 (mmp) cc_final: 0.7818 (tmm) REVERT: A 357 MET cc_start: 0.7486 (tpt) cc_final: 0.7186 (tpp) REVERT: A 448 LEU cc_start: 0.9440 (tp) cc_final: 0.8771 (tp) REVERT: A 452 PHE cc_start: 0.8609 (m-10) cc_final: 0.8182 (m-80) REVERT: A 633 MET cc_start: 0.8326 (tpt) cc_final: 0.7823 (tpp) REVERT: A 665 LYS cc_start: 0.8982 (tptp) cc_final: 0.8570 (tppt) REVERT: A 669 ASP cc_start: 0.7742 (m-30) cc_final: 0.7480 (m-30) REVERT: B 121 ILE cc_start: 0.9265 (pt) cc_final: 0.9028 (mm) REVERT: B 180 MET cc_start: 0.8753 (tpp) cc_final: 0.8212 (mmm) REVERT: B 196 CYS cc_start: 0.8649 (p) cc_final: 0.8430 (p) REVERT: B 299 MET cc_start: 0.8377 (mmp) cc_final: 0.7973 (tmm) REVERT: B 452 PHE cc_start: 0.8406 (m-10) cc_final: 0.8187 (t80) REVERT: B 633 MET cc_start: 0.8483 (tpt) cc_final: 0.7878 (tpp) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.2029 time to fit residues: 46.6922 Evaluate side-chains 123 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 50.0000 chunk 74 optimal weight: 0.0870 chunk 96 optimal weight: 8.9990 chunk 110 optimal weight: 9.9990 chunk 73 optimal weight: 20.0000 chunk 131 optimal weight: 7.9990 chunk 82 optimal weight: 40.0000 chunk 79 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 overall best weight: 5.8166 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10688 Z= 0.194 Angle : 0.555 6.940 14532 Z= 0.277 Chirality : 0.044 0.157 1728 Planarity : 0.004 0.046 1808 Dihedral : 3.627 18.396 1456 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: 1.99 (0.24), residues: 1352 helix: 1.95 (0.18), residues: 908 sheet: 2.80 (0.88), residues: 38 loop : -0.24 (0.34), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 699 HIS 0.005 0.001 HIS B 25 PHE 0.012 0.001 PHE A 452 TYR 0.020 0.001 TYR A 552 ARG 0.005 0.000 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.8534 (ppp) cc_final: 0.8268 (ppp) REVERT: A 132 ILE cc_start: 0.8397 (pt) cc_final: 0.8152 (pt) REVERT: A 299 MET cc_start: 0.8309 (mmp) cc_final: 0.7848 (tmm) REVERT: A 357 MET cc_start: 0.7523 (tpt) cc_final: 0.7187 (tpp) REVERT: A 452 PHE cc_start: 0.8431 (m-10) cc_final: 0.8204 (t80) REVERT: A 484 LEU cc_start: 0.8849 (mt) cc_final: 0.8167 (tt) REVERT: A 633 MET cc_start: 0.8289 (tpt) cc_final: 0.7827 (tpp) REVERT: A 665 LYS cc_start: 0.8998 (tptp) cc_final: 0.8771 (tppt) REVERT: B 121 ILE cc_start: 0.9270 (pt) cc_final: 0.9037 (mm) REVERT: B 132 ILE cc_start: 0.8662 (pt) cc_final: 0.8454 (pt) REVERT: B 180 MET cc_start: 0.8700 (tpp) cc_final: 0.8155 (mmm) REVERT: B 196 CYS cc_start: 0.8678 (p) cc_final: 0.8472 (p) REVERT: B 299 MET cc_start: 0.8373 (mmp) cc_final: 0.7996 (tmm) REVERT: B 452 PHE cc_start: 0.8384 (m-10) cc_final: 0.8071 (t80) REVERT: B 633 MET cc_start: 0.8440 (tpt) cc_final: 0.7838 (tpp) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2001 time to fit residues: 47.7877 Evaluate side-chains 124 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 83 optimal weight: 0.4980 chunk 89 optimal weight: 10.0000 chunk 64 optimal weight: 0.0000 chunk 12 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 chunk 119 optimal weight: 0.0970 chunk 125 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN B 648 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10688 Z= 0.134 Angle : 0.536 7.239 14532 Z= 0.262 Chirality : 0.043 0.148 1728 Planarity : 0.004 0.038 1808 Dihedral : 3.507 18.678 1456 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.09 % Allowed : 0.62 % Favored : 99.29 % 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: 2.01 (0.25), residues: 1352 helix: 1.95 (0.18), residues: 908 sheet: 2.97 (0.89), residues: 38 loop : -0.21 (0.34), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 70 HIS 0.004 0.001 HIS A 25 PHE 0.009 0.001 PHE B 351 TYR 0.018 0.001 TYR A 552 ARG 0.005 0.000 ARG A 691 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.8509 (ppp) cc_final: 0.8238 (ppp) REVERT: A 132 ILE cc_start: 0.8366 (pt) cc_final: 0.8022 (pt) REVERT: A 299 MET cc_start: 0.8305 (mmp) cc_final: 0.7845 (tmm) REVERT: A 357 MET cc_start: 0.7426 (tpt) cc_final: 0.7057 (tpp) REVERT: A 440 LEU cc_start: 0.8985 (mm) cc_final: 0.8388 (tp) REVERT: A 452 PHE cc_start: 0.8413 (m-10) cc_final: 0.8167 (t80) REVERT: A 484 LEU cc_start: 0.8841 (mt) cc_final: 0.8091 (tt) REVERT: A 633 MET cc_start: 0.8225 (tpt) cc_final: 0.7773 (tpp) REVERT: A 665 LYS cc_start: 0.9015 (tptp) cc_final: 0.8571 (tppt) REVERT: A 669 ASP cc_start: 0.7612 (m-30) cc_final: 0.7314 (m-30) REVERT: B 121 ILE cc_start: 0.9240 (pt) cc_final: 0.9017 (mm) REVERT: B 180 MET cc_start: 0.8682 (tpp) cc_final: 0.7899 (mmm) REVERT: B 196 CYS cc_start: 0.8650 (p) cc_final: 0.8417 (p) REVERT: B 299 MET cc_start: 0.8370 (mmp) cc_final: 0.7950 (tmm) REVERT: B 452 PHE cc_start: 0.8369 (m-10) cc_final: 0.8011 (t80) REVERT: B 633 MET cc_start: 0.8380 (tpt) cc_final: 0.7804 (tpp) outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.1970 time to fit residues: 47.6179 Evaluate side-chains 133 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 1.9990 chunk 125 optimal weight: 0.1980 chunk 73 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 95 optimal weight: 50.0000 chunk 37 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10688 Z= 0.136 Angle : 0.545 7.337 14532 Z= 0.267 Chirality : 0.043 0.153 1728 Planarity : 0.004 0.038 1808 Dihedral : 3.444 17.817 1456 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: 2.01 (0.25), residues: 1352 helix: 1.98 (0.18), residues: 902 sheet: 3.10 (0.89), residues: 38 loop : -0.28 (0.34), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 70 HIS 0.006 0.001 HIS A 25 PHE 0.028 0.001 PHE B 351 TYR 0.024 0.001 TYR B 552 ARG 0.006 0.000 ARG A 691 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.8520 (ppp) cc_final: 0.8277 (ppp) REVERT: A 132 ILE cc_start: 0.8309 (pt) cc_final: 0.8063 (pt) REVERT: A 299 MET cc_start: 0.8301 (mmp) cc_final: 0.7837 (tmm) REVERT: A 357 MET cc_start: 0.7497 (tpt) cc_final: 0.7123 (tpp) REVERT: A 452 PHE cc_start: 0.8468 (m-10) cc_final: 0.8231 (t80) REVERT: A 484 LEU cc_start: 0.8856 (mt) cc_final: 0.8150 (tt) REVERT: A 633 MET cc_start: 0.8222 (tpt) cc_final: 0.7774 (tpp) REVERT: A 665 LYS cc_start: 0.9038 (tptp) cc_final: 0.8548 (tppt) REVERT: A 669 ASP cc_start: 0.7594 (m-30) cc_final: 0.6997 (m-30) REVERT: B 121 ILE cc_start: 0.9234 (pt) cc_final: 0.9017 (mm) REVERT: B 132 ILE cc_start: 0.8593 (pt) cc_final: 0.8318 (pt) REVERT: B 180 MET cc_start: 0.8791 (tpp) cc_final: 0.8129 (mmm) REVERT: B 196 CYS cc_start: 0.8652 (p) cc_final: 0.8390 (p) REVERT: B 299 MET cc_start: 0.8358 (mmp) cc_final: 0.7940 (tmm) REVERT: B 452 PHE cc_start: 0.8414 (m-10) cc_final: 0.8016 (t80) REVERT: B 633 MET cc_start: 0.8362 (tpt) cc_final: 0.7797 (tpp) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1794 time to fit residues: 44.1847 Evaluate side-chains 131 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 135 optimal weight: 0.7980 chunk 124 optimal weight: 30.0000 chunk 107 optimal weight: 0.8980 chunk 11 optimal weight: 0.0030 chunk 83 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 85 optimal weight: 50.0000 chunk 114 optimal weight: 10.0000 overall best weight: 2.9394 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10688 Z= 0.146 Angle : 0.545 7.418 14532 Z= 0.267 Chirality : 0.043 0.213 1728 Planarity : 0.004 0.038 1808 Dihedral : 3.444 17.566 1456 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 2.03 (0.25), residues: 1352 helix: 2.00 (0.18), residues: 902 sheet: 3.13 (0.89), residues: 38 loop : -0.28 (0.34), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 70 HIS 0.006 0.001 HIS A 25 PHE 0.040 0.001 PHE B 351 TYR 0.022 0.001 TYR B 552 ARG 0.005 0.000 ARG A 691 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.8548 (ppp) cc_final: 0.8305 (ppp) REVERT: A 132 ILE cc_start: 0.8317 (pt) cc_final: 0.7993 (pt) REVERT: A 299 MET cc_start: 0.8304 (mmp) cc_final: 0.7832 (tmm) REVERT: A 357 MET cc_start: 0.7451 (tpt) cc_final: 0.7075 (tpp) REVERT: A 452 PHE cc_start: 0.8529 (m-10) cc_final: 0.8140 (m-80) REVERT: A 484 LEU cc_start: 0.8845 (mt) cc_final: 0.8075 (tt) REVERT: A 633 MET cc_start: 0.8219 (tpt) cc_final: 0.7773 (tpp) REVERT: A 665 LYS cc_start: 0.9056 (tptp) cc_final: 0.8650 (tppt) REVERT: B 180 MET cc_start: 0.8766 (tpp) cc_final: 0.8106 (mmm) REVERT: B 196 CYS cc_start: 0.8648 (p) cc_final: 0.8399 (p) REVERT: B 276 LYS cc_start: 0.7992 (tttt) cc_final: 0.7581 (ptmt) REVERT: B 299 MET cc_start: 0.8369 (mmp) cc_final: 0.7932 (tmm) REVERT: B 445 ILE cc_start: 0.8816 (mm) cc_final: 0.8609 (mm) REVERT: B 452 PHE cc_start: 0.8464 (m-10) cc_final: 0.7847 (m-80) REVERT: B 633 MET cc_start: 0.8363 (tpt) cc_final: 0.7794 (tpp) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1837 time to fit residues: 43.2298 Evaluate side-chains 125 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 0.8980 chunk 99 optimal weight: 40.0000 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 30.0000 chunk 108 optimal weight: 6.9990 chunk 45 optimal weight: 0.0570 chunk 110 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 94 optimal weight: 40.0000 chunk 6 optimal weight: 0.0270 overall best weight: 2.3960 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.079733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.056758 restraints weight = 50731.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.058731 restraints weight = 27112.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.060006 restraints weight = 18035.192| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10688 Z= 0.141 Angle : 0.545 6.607 14532 Z= 0.267 Chirality : 0.043 0.168 1728 Planarity : 0.004 0.038 1808 Dihedral : 3.427 18.000 1456 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: 2.04 (0.25), residues: 1352 helix: 1.99 (0.18), residues: 904 sheet: 3.17 (0.89), residues: 38 loop : -0.24 (0.34), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 70 HIS 0.005 0.001 HIS A 25 PHE 0.046 0.001 PHE B 351 TYR 0.022 0.001 TYR B 552 ARG 0.005 0.000 ARG A 691 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2209.33 seconds wall clock time: 40 minutes 15.00 seconds (2415.00 seconds total)