Starting phenix.real_space_refine on Thu Nov 14 21:37:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3h_36851/11_2024/8k3h_36851.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3h_36851/11_2024/8k3h_36851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3h_36851/11_2024/8k3h_36851.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3h_36851/11_2024/8k3h_36851.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3h_36851/11_2024/8k3h_36851.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3h_36851/11_2024/8k3h_36851.cif" } resolution = 2.86 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= 0.005 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 P 6 5.49 5 S 24 5.16 5 C 4724 2.51 5 N 1314 2.21 5 O 1392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7460 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3686 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 456} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 75 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 4, 'HIS:plan': 1, 'LLP:plan-2': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 82 Chain: "B" Number of atoms: 3686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3686 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 456} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 75 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 4, 'HIS:plan': 1, 'LLP:plan-2': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 82 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.77, per 1000 atoms: 0.64 Number of scatterers: 7460 At special positions: 0 Unit cell: (73.87, 100.43, 78.02, 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) S 24 16.00 P 6 15.00 O 1392 8.00 N 1314 7.00 C 4724 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: 1.86 Conformation dependent library (CDL) restraints added in 1.1 seconds 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1788 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 8 sheets defined 55.9% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 337 through 347 removed outlier: 3.534A pdb=" N LEU A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL A 343 " --> pdb=" O ARG A 339 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 347 " --> pdb=" O VAL A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 368 removed outlier: 3.561A pdb=" N LEU A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 384 removed outlier: 3.793A pdb=" N ALA A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 397 Processing helix chain 'A' and resid 398 through 415 removed outlier: 3.880A pdb=" N VAL A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 413 " --> pdb=" O PHE A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 455 removed outlier: 3.517A pdb=" N THR A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 480 removed outlier: 3.566A pdb=" N VAL A 479 " --> pdb=" O ALA A 475 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER A 480 " --> pdb=" O MET A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 489 No H-bonds generated for 'chain 'A' and resid 487 through 489' Processing helix chain 'A' and resid 496 through 509 Processing helix chain 'A' and resid 525 through 536 removed outlier: 3.857A pdb=" N ARG A 535 " --> pdb=" O SER A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 559 Processing helix chain 'A' and resid 580 through 590 Processing helix chain 'A' and resid 613 through 618 Processing helix chain 'A' and resid 633 through 637 removed outlier: 3.534A pdb=" N LYS A 637 " --> pdb=" O PRO A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 659 removed outlier: 4.296A pdb=" N GLU A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE A 654 " --> pdb=" O ARG A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 665 No H-bonds generated for 'chain 'A' and resid 663 through 665' Processing helix chain 'A' and resid 666 through 682 Processing helix chain 'A' and resid 688 through 693 Processing helix chain 'A' and resid 694 through 695 No H-bonds generated for 'chain 'A' and resid 694 through 695' Processing helix chain 'A' and resid 696 through 700 removed outlier: 3.604A pdb=" N TYR A 699 " --> pdb=" O SER A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 738 removed outlier: 3.539A pdb=" N ALA A 738 " --> pdb=" O CYS A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 772 Processing helix chain 'A' and resid 780 through 783 Processing helix chain 'A' and resid 797 through 811 Processing helix chain 'B' and resid 337 through 347 removed outlier: 3.532A pdb=" N LEU B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL B 343 " --> pdb=" O ARG B 339 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE B 344 " --> pdb=" O THR B 340 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA B 347 " --> pdb=" O VAL B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 368 removed outlier: 3.559A pdb=" N LEU B 368 " --> pdb=" O VAL B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 384 removed outlier: 3.785A pdb=" N ALA B 378 " --> pdb=" O ARG B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 397 Processing helix chain 'B' and resid 398 through 415 removed outlier: 3.880A pdb=" N VAL B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE B 413 " --> pdb=" O PHE B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 455 removed outlier: 3.517A pdb=" N THR B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 480 removed outlier: 3.568A pdb=" N VAL B 479 " --> pdb=" O ALA B 475 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER B 480 " --> pdb=" O MET B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 489 No H-bonds generated for 'chain 'B' and resid 487 through 489' Processing helix chain 'B' and resid 496 through 509 Processing helix chain 'B' and resid 525 through 536 removed outlier: 3.854A pdb=" N ARG B 535 " --> pdb=" O SER B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 559 Processing helix chain 'B' and resid 580 through 590 Processing helix chain 'B' and resid 613 through 618 Processing helix chain 'B' and resid 633 through 637 removed outlier: 3.523A pdb=" N LYS B 637 " --> pdb=" O PRO B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 659 removed outlier: 4.295A pdb=" N GLU B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE B 654 " --> pdb=" O ARG B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 682 Processing helix chain 'B' and resid 688 through 693 Processing helix chain 'B' and resid 694 through 695 No H-bonds generated for 'chain 'B' and resid 694 through 695' Processing helix chain 'B' and resid 696 through 700 removed outlier: 3.605A pdb=" N TYR B 699 " --> pdb=" O SER B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 738 removed outlier: 3.501A pdb=" N ALA B 738 " --> pdb=" O CYS B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 772 Processing helix chain 'B' and resid 780 through 783 Processing helix chain 'B' and resid 797 through 811 Processing sheet with id=AA1, first strand: chain 'A' and resid 427 through 428 removed outlier: 6.678A pdb=" N ILE A 427 " --> pdb=" O SER A 775 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 491 through 494 removed outlier: 3.667A pdb=" N TRP A 640 " --> pdb=" O SER A 625 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE A 597 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL A 624 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU A 599 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N SER A 626 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL A 566 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASP A 600 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU A 568 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N GLN A 569 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA A 518 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL A 541 " --> pdb=" O ALA A 518 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N CYS A 520 " --> pdb=" O VAL A 541 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 545 through 546 Processing sheet with id=AA4, first strand: chain 'A' and resid 741 through 742 Processing sheet with id=AA5, first strand: chain 'B' and resid 427 through 428 removed outlier: 6.685A pdb=" N ILE B 427 " --> pdb=" O SER B 775 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 491 through 494 removed outlier: 3.668A pdb=" N TRP B 640 " --> pdb=" O SER B 625 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE B 597 " --> pdb=" O ILE B 622 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL B 624 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU B 599 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N SER B 626 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL B 566 " --> pdb=" O ILE B 598 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ASP B 600 " --> pdb=" O VAL B 566 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU B 568 " --> pdb=" O ASP B 600 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLN B 569 " --> pdb=" O ALA B 521 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA B 518 " --> pdb=" O LEU B 539 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL B 541 " --> pdb=" O ALA B 518 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N CYS B 520 " --> pdb=" O VAL B 541 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 545 through 546 Processing sheet with id=AA8, first strand: chain 'B' and resid 741 through 742 370 hydrogen bonds defined for protein. 1044 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: 2.22 Time building geometry restraints manager: 2.14 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: 2458 1.34 - 1.46: 1791 1.46 - 1.58: 3341 1.58 - 1.69: 10 1.69 - 1.81: 38 Bond restraints: 7638 Sorted by residual: bond pdb=" OP4 LLP B 629 " pdb=" P LLP B 629 " ideal model delta sigma weight residual 1.726 1.613 0.113 2.00e-02 2.50e+03 3.16e+01 bond pdb=" OP4 LLP A 629 " pdb=" P LLP A 629 " ideal model delta sigma weight residual 1.726 1.614 0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" C5' LLP A 629 " pdb=" OP4 LLP A 629 " ideal model delta sigma weight residual 1.396 1.462 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C5' LLP B 629 " pdb=" OP4 LLP B 629 " ideal model delta sigma weight residual 1.396 1.462 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" O3 NAD B 901 " pdb=" PA NAD B 901 " ideal model delta sigma weight residual 1.653 1.607 0.046 2.00e-02 2.50e+03 5.27e+00 ... (remaining 7633 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 10251 1.70 - 3.40: 127 3.40 - 5.09: 36 5.09 - 6.79: 8 6.79 - 8.49: 2 Bond angle restraints: 10424 Sorted by residual: angle pdb=" PA NAD B 901 " pdb=" O3 NAD B 901 " pdb=" PN NAD B 901 " ideal model delta sigma weight residual 126.50 134.99 -8.49 3.00e+00 1.11e-01 8.01e+00 angle pdb=" PA NAD A 901 " pdb=" O3 NAD A 901 " pdb=" PN NAD A 901 " ideal model delta sigma weight residual 126.50 134.98 -8.48 3.00e+00 1.11e-01 7.99e+00 angle pdb=" N PRO B 526 " pdb=" CA PRO B 526 " pdb=" C PRO B 526 " ideal model delta sigma weight residual 110.70 113.27 -2.57 1.22e+00 6.72e-01 4.45e+00 angle pdb=" N PRO A 526 " pdb=" CA PRO A 526 " pdb=" C PRO A 526 " ideal model delta sigma weight residual 110.70 113.27 -2.57 1.22e+00 6.72e-01 4.45e+00 angle pdb=" C2D NAD B 901 " pdb=" C1D NAD B 901 " pdb=" O4D NAD B 901 " ideal model delta sigma weight residual 105.82 99.58 6.24 3.00e+00 1.11e-01 4.32e+00 ... (remaining 10419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 4101 17.14 - 34.28: 361 34.28 - 51.42: 65 51.42 - 68.56: 25 68.56 - 85.70: 28 Dihedral angle restraints: 4580 sinusoidal: 1798 harmonic: 2782 Sorted by residual: dihedral pdb=" CA ASP B 760 " pdb=" CB ASP B 760 " pdb=" CG ASP B 760 " pdb=" OD1 ASP B 760 " ideal model delta sinusoidal sigma weight residual -30.00 -84.44 54.44 1 2.00e+01 2.50e-03 1.00e+01 dihedral pdb=" CA ASP A 760 " pdb=" CB ASP A 760 " pdb=" CG ASP A 760 " pdb=" OD1 ASP A 760 " ideal model delta sinusoidal sigma weight residual -30.00 -84.40 54.40 1 2.00e+01 2.50e-03 1.00e+01 dihedral pdb=" O2B NAD A 901 " pdb=" C2B NAD A 901 " pdb=" C3B NAD A 901 " pdb=" O3B NAD A 901 " ideal model delta sinusoidal sigma weight residual -45.60 40.10 -85.70 1 3.00e+01 1.11e-03 9.87e+00 ... (remaining 4577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 947 0.046 - 0.092: 164 0.092 - 0.138: 63 0.138 - 0.184: 4 0.184 - 0.230: 2 Chirality restraints: 1180 Sorted by residual: chirality pdb=" C1D NAD B 901 " pdb=" C2D NAD B 901 " pdb=" N1N NAD B 901 " pdb=" O4D NAD B 901 " both_signs ideal model delta sigma weight residual False 2.41 2.64 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" C1D NAD A 901 " pdb=" C2D NAD A 901 " pdb=" N1N NAD A 901 " pdb=" O4D NAD A 901 " both_signs ideal model delta sigma weight residual False 2.41 2.64 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C3B NAD B 901 " pdb=" C2B NAD B 901 " pdb=" C4B NAD B 901 " pdb=" O3B NAD B 901 " both_signs ideal model delta sigma weight residual False -2.71 -2.54 -0.17 2.00e-01 2.50e+01 7.60e-01 ... (remaining 1177 not shown) Planarity restraints: 1330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP A 629 " 0.039 2.00e-02 2.50e+03 4.01e-02 1.60e+01 pdb=" NZ LLP A 629 " -0.033 2.00e-02 2.50e+03 pdb=" C4 LLP A 629 " 0.041 2.00e-02 2.50e+03 pdb=" C4' LLP A 629 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP B 629 " -0.038 2.00e-02 2.50e+03 3.98e-02 1.59e+01 pdb=" NZ LLP B 629 " 0.033 2.00e-02 2.50e+03 pdb=" C4 LLP B 629 " -0.041 2.00e-02 2.50e+03 pdb=" C4' LLP B 629 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD B 901 " -0.024 2.00e-02 2.50e+03 1.76e-02 6.17e+00 pdb=" C2N NAD B 901 " 0.038 2.00e-02 2.50e+03 pdb=" C3N NAD B 901 " 0.003 2.00e-02 2.50e+03 pdb=" C4N NAD B 901 " -0.010 2.00e-02 2.50e+03 pdb=" C5N NAD B 901 " 0.002 2.00e-02 2.50e+03 pdb=" C6N NAD B 901 " 0.003 2.00e-02 2.50e+03 pdb=" C7N NAD B 901 " -0.017 2.00e-02 2.50e+03 pdb=" N1N NAD B 901 " 0.005 2.00e-02 2.50e+03 ... (remaining 1327 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1369 2.77 - 3.30: 6866 3.30 - 3.83: 12772 3.83 - 4.37: 15742 4.37 - 4.90: 26717 Nonbonded interactions: 63466 Sorted by model distance: nonbonded pdb=" OG1 THR B 550 " pdb=" OG SER B 577 " model vdw 2.237 3.040 nonbonded pdb=" OG1 THR A 550 " pdb=" OG SER A 577 " model vdw 2.237 3.040 nonbonded pdb=" O GLY B 496 " pdb=" OG1 THR B 500 " model vdw 2.322 3.040 nonbonded pdb=" O GLY A 496 " pdb=" OG1 THR A 500 " model vdw 2.330 3.040 nonbonded pdb=" O HIS A 485 " pdb=" NE2 GLN A 617 " model vdw 2.338 3.120 ... (remaining 63461 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: 0.010 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.600 Find NCS groups from input model: 0.210 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:12.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 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 : 0.003 0.113 7638 Z= 0.221 Angle : 0.522 8.491 10424 Z= 0.237 Chirality : 0.041 0.230 1180 Planarity : 0.004 0.040 1330 Dihedral : 15.584 85.705 2792 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.44 (0.27), residues: 950 helix: 0.69 (0.24), residues: 458 sheet: 0.27 (0.44), residues: 122 loop : -0.02 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 679 HIS 0.001 0.000 HIS A 712 PHE 0.009 0.001 PHE B 409 TYR 0.007 0.001 TYR A 525 ARG 0.002 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.858 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 1.6034 time to fit residues: 114.5104 Evaluate side-chains 55 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 ASN B 512 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7638 Z= 0.183 Angle : 0.503 6.705 10424 Z= 0.256 Chirality : 0.041 0.135 1180 Planarity : 0.004 0.036 1330 Dihedral : 9.735 57.616 1194 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.19 % Allowed : 4.88 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.17 (0.28), residues: 950 helix: 1.58 (0.24), residues: 484 sheet: 0.15 (0.43), residues: 122 loop : -0.03 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 798 HIS 0.003 0.001 HIS A 485 PHE 0.019 0.002 PHE B 641 TYR 0.011 0.001 TYR A 458 ARG 0.003 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.826 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 60 average time/residue: 1.5728 time to fit residues: 99.1549 Evaluate side-chains 53 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 718 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 59 optimal weight: 0.0170 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7638 Z= 0.152 Angle : 0.463 6.243 10424 Z= 0.233 Chirality : 0.040 0.136 1180 Planarity : 0.004 0.036 1330 Dihedral : 7.947 54.684 1194 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.06 % Allowed : 8.31 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.51 (0.28), residues: 950 helix: 1.98 (0.24), residues: 488 sheet: 0.14 (0.43), residues: 122 loop : -0.02 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 798 HIS 0.001 0.000 HIS B 485 PHE 0.017 0.002 PHE A 641 TYR 0.007 0.001 TYR A 458 ARG 0.003 0.000 ARG B 387 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.838 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 52 average time/residue: 1.4705 time to fit residues: 81.1859 Evaluate side-chains 54 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 718 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 41 optimal weight: 0.0000 chunk 58 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 92 optimal weight: 0.0980 chunk 83 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7638 Z= 0.163 Angle : 0.477 6.608 10424 Z= 0.240 Chirality : 0.040 0.135 1180 Planarity : 0.004 0.035 1330 Dihedral : 7.542 57.449 1194 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.19 % Allowed : 9.50 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.62 (0.28), residues: 950 helix: 2.12 (0.24), residues: 488 sheet: 0.15 (0.43), residues: 122 loop : -0.05 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 798 HIS 0.001 0.000 HIS B 712 PHE 0.019 0.002 PHE A 641 TYR 0.007 0.001 TYR A 458 ARG 0.003 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.879 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 49 average time/residue: 1.6126 time to fit residues: 83.3370 Evaluate side-chains 53 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 565 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 5.9990 chunk 1 optimal weight: 0.0980 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 31 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7638 Z= 0.138 Angle : 0.452 6.642 10424 Z= 0.228 Chirality : 0.040 0.135 1180 Planarity : 0.004 0.034 1330 Dihedral : 7.264 53.561 1194 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.79 % Allowed : 10.03 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.73 (0.28), residues: 950 helix: 2.22 (0.24), residues: 488 sheet: 0.21 (0.44), residues: 122 loop : -0.01 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 798 HIS 0.001 0.000 HIS A 536 PHE 0.017 0.001 PHE A 641 TYR 0.006 0.001 TYR A 458 ARG 0.007 0.000 ARG B 414 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.907 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 48 average time/residue: 1.6701 time to fit residues: 84.6293 Evaluate side-chains 50 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 565 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 3.9990 chunk 18 optimal weight: 0.1980 chunk 54 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7638 Z= 0.173 Angle : 0.475 6.795 10424 Z= 0.239 Chirality : 0.040 0.134 1180 Planarity : 0.004 0.034 1330 Dihedral : 7.407 56.671 1194 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.06 % Allowed : 10.29 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.70 (0.28), residues: 950 helix: 2.21 (0.24), residues: 488 sheet: 0.18 (0.44), residues: 122 loop : -0.04 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 798 HIS 0.001 0.000 HIS A 536 PHE 0.020 0.002 PHE A 641 TYR 0.006 0.001 TYR A 458 ARG 0.005 0.000 ARG B 414 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 1.334 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 50 average time/residue: 1.6768 time to fit residues: 88.5623 Evaluate side-chains 54 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 633 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 42 optimal weight: 0.4980 chunk 36 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7638 Z= 0.245 Angle : 0.529 7.568 10424 Z= 0.266 Chirality : 0.042 0.134 1180 Planarity : 0.004 0.035 1330 Dihedral : 7.861 62.696 1194 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.06 % Allowed : 10.95 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.54 (0.28), residues: 950 helix: 2.11 (0.25), residues: 486 sheet: 0.33 (0.43), residues: 118 loop : -0.26 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 798 HIS 0.002 0.001 HIS A 603 PHE 0.022 0.002 PHE A 641 TYR 0.007 0.001 TYR B 514 ARG 0.005 0.000 ARG B 414 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.849 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 48 average time/residue: 1.6339 time to fit residues: 82.6228 Evaluate side-chains 50 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 633 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.4980 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 63 optimal weight: 0.0040 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7638 Z= 0.199 Angle : 0.500 7.477 10424 Z= 0.251 Chirality : 0.041 0.133 1180 Planarity : 0.004 0.034 1330 Dihedral : 7.626 60.064 1194 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.19 % Allowed : 10.82 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.56 (0.28), residues: 950 helix: 2.08 (0.24), residues: 490 sheet: 0.36 (0.43), residues: 118 loop : -0.21 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 798 HIS 0.001 0.000 HIS A 536 PHE 0.020 0.002 PHE A 641 TYR 0.007 0.001 TYR A 514 ARG 0.005 0.000 ARG B 414 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.825 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 51 average time/residue: 1.8039 time to fit residues: 96.5316 Evaluate side-chains 55 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 633 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 0.0470 chunk 77 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7638 Z= 0.144 Angle : 0.467 7.468 10424 Z= 0.234 Chirality : 0.040 0.135 1180 Planarity : 0.004 0.034 1330 Dihedral : 7.276 54.890 1194 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.06 % Allowed : 11.08 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.70 (0.28), residues: 950 helix: 2.19 (0.25), residues: 490 sheet: 0.21 (0.43), residues: 122 loop : -0.04 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 798 HIS 0.001 0.000 HIS B 712 PHE 0.017 0.001 PHE B 641 TYR 0.006 0.001 TYR B 713 ARG 0.007 0.000 ARG B 414 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.906 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 51 average time/residue: 1.7793 time to fit residues: 95.1156 Evaluate side-chains 51 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 633 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 663 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 7638 Z= 0.393 Angle : 0.615 8.551 10424 Z= 0.309 Chirality : 0.046 0.140 1180 Planarity : 0.005 0.039 1330 Dihedral : 8.404 69.085 1194 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.06 % Allowed : 11.08 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.26 (0.28), residues: 950 helix: 1.84 (0.24), residues: 488 sheet: 0.29 (0.42), residues: 118 loop : -0.36 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 631 HIS 0.003 0.001 HIS A 603 PHE 0.026 0.003 PHE B 641 TYR 0.009 0.002 TYR A 514 ARG 0.006 0.001 ARG A 510 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.841 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 43 average time/residue: 1.8062 time to fit residues: 81.6737 Evaluate side-chains 45 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 633 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.110736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.094581 restraints weight = 8680.820| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.19 r_work: 0.2814 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7638 Z= 0.166 Angle : 0.485 7.469 10424 Z= 0.244 Chirality : 0.040 0.132 1180 Planarity : 0.004 0.034 1330 Dihedral : 7.478 58.258 1194 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.06 % Allowed : 11.08 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.51 (0.28), residues: 950 helix: 2.07 (0.25), residues: 490 sheet: 0.07 (0.43), residues: 122 loop : -0.17 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 798 HIS 0.001 0.000 HIS A 603 PHE 0.019 0.002 PHE A 641 TYR 0.007 0.001 TYR B 514 ARG 0.006 0.000 ARG B 414 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2333.22 seconds wall clock time: 42 minutes 43.91 seconds (2563.91 seconds total)