Starting phenix.real_space_refine on Fri Aug 22 19:56:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k3h_36851/08_2025/8k3h_36851.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3h_36851/08_2025/8k3h_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 { model { file = "/net/cci-nas-00/data/ceres_data/8k3h_36851/08_2025/8k3h_36851.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3h_36851/08_2025/8k3h_36851.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k3h_36851/08_2025/8k3h_36851.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3h_36851/08_2025/8k3h_36851.map" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 7, 'ASP:plan': 4, 'ARG:plan': 4, 'GLN:plan1': 4, 'HIS:plan': 1, 'LLP:plan-2': 1} 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: {'GLU:plan': 7, 'ASP:plan': 4, 'ARG:plan': 4, 'GLN:plan1': 4, 'HIS:plan': 1, 'LLP:plan-2': 1} 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: 2.12, per 1000 atoms: 0.28 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: 0.63 Conformation dependent library (CDL) restraints added in 473.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.31 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: 1.30 Time building geometry restraints manager: 0.84 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 9.250 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.920 ------------------------------------------------------------------------------- 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= 0.170 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 : 3.88 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A 455 TYR 0.007 0.001 TYR A 525 PHE 0.009 0.001 PHE B 409 TRP 0.004 0.001 TRP B 679 HIS 0.001 0.000 HIS A 712 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 7638) covalent geometry : angle 0.52170 (10424) hydrogen bonds : bond 0.24009 ( 370) hydrogen bonds : angle 6.41295 ( 1044) *********************** 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 : 0.306 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.8433 time to fit residues: 60.0473 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 : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.0870 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.111220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.094989 restraints weight = 8785.721| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.23 r_work: 0.2825 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7638 Z= 0.128 Angle : 0.499 6.677 10424 Z= 0.256 Chirality : 0.041 0.138 1180 Planarity : 0.004 0.035 1330 Dihedral : 9.970 55.078 1194 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.79 % Allowed : 5.54 % Favored : 93.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.28), residues: 950 helix: 1.61 (0.24), residues: 484 sheet: 0.14 (0.43), residues: 122 loop : -0.04 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 510 TYR 0.010 0.001 TYR A 458 PHE 0.020 0.002 PHE B 641 TRP 0.008 0.001 TRP A 798 HIS 0.003 0.001 HIS B 485 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 7638) covalent geometry : angle 0.49901 (10424) hydrogen bonds : bond 0.05097 ( 370) hydrogen bonds : angle 4.51993 ( 1044) *********************** 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 63 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.311 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 59 average time/residue: 0.8624 time to fit residues: 53.1932 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 : 0.307 ------------------------------------------------------------------------------- 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 44 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3121 r_free = 0.3121 target = 0.109392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.093012 restraints weight = 8762.244| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.22 r_work: 0.2794 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7638 Z= 0.142 Angle : 0.514 6.825 10424 Z= 0.259 Chirality : 0.042 0.135 1180 Planarity : 0.004 0.036 1330 Dihedral : 8.478 63.069 1194 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.32 % Allowed : 8.18 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.28), residues: 950 helix: 1.81 (0.24), residues: 488 sheet: 0.23 (0.42), residues: 118 loop : -0.17 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 387 TYR 0.010 0.001 TYR B 525 PHE 0.020 0.002 PHE A 641 TRP 0.007 0.001 TRP A 798 HIS 0.001 0.000 HIS A 603 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 7638) covalent geometry : angle 0.51397 (10424) hydrogen bonds : bond 0.04576 ( 370) hydrogen bonds : angle 4.23662 ( 1044) *********************** 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 57 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.306 Fit side-chains REVERT: A 414 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7961 (ptt90) REVERT: A 800 ASP cc_start: 0.7873 (m-30) cc_final: 0.7514 (t0) REVERT: B 414 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7997 (ptt90) REVERT: B 800 ASP cc_start: 0.7884 (m-30) cc_final: 0.7505 (t0) outliers start: 10 outliers final: 4 residues processed: 51 average time/residue: 0.8365 time to fit residues: 44.7508 Evaluate side-chains 51 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 414 ARG 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 33 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3145 r_free = 0.3145 target = 0.111079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.094675 restraints weight = 8899.326| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 1.23 r_work: 0.2813 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1503 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= 0.110 Angle : 0.475 6.631 10424 Z= 0.239 Chirality : 0.040 0.135 1180 Planarity : 0.004 0.035 1330 Dihedral : 7.728 56.706 1194 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.06 % Allowed : 9.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.28), residues: 950 helix: 1.99 (0.24), residues: 488 sheet: 0.07 (0.43), residues: 122 loop : -0.09 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 510 TYR 0.007 0.001 TYR A 458 PHE 0.018 0.002 PHE B 641 TRP 0.005 0.001 TRP B 798 HIS 0.001 0.000 HIS B 712 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 7638) covalent geometry : angle 0.47524 (10424) hydrogen bonds : bond 0.03871 ( 370) hydrogen bonds : angle 4.05350 ( 1044) *********************** 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 53 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.323 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 47 average time/residue: 0.8259 time to fit residues: 40.7827 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 : 0.274 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 80 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 chunk 33 optimal weight: 0.0980 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3161 r_free = 0.3161 target = 0.112161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.095796 restraints weight = 8799.938| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.22 r_work: 0.2829 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1563 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= 0.096 Angle : 0.457 6.732 10424 Z= 0.229 Chirality : 0.040 0.136 1180 Planarity : 0.004 0.034 1330 Dihedral : 7.351 54.775 1194 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.32 % Allowed : 10.16 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.28), residues: 950 helix: 2.15 (0.24), residues: 488 sheet: 0.11 (0.43), residues: 122 loop : -0.09 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 414 TYR 0.006 0.001 TYR A 458 PHE 0.018 0.001 PHE A 641 TRP 0.006 0.001 TRP B 798 HIS 0.001 0.000 HIS B 712 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 7638) covalent geometry : angle 0.45713 (10424) hydrogen bonds : bond 0.03543 ( 370) hydrogen bonds : angle 3.90215 ( 1044) *********************** 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 56 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.274 Fit side-chains REVERT: A 800 ASP cc_start: 0.7786 (m-30) cc_final: 0.7527 (t0) REVERT: B 800 ASP cc_start: 0.7781 (m-30) cc_final: 0.7545 (t0) outliers start: 10 outliers final: 6 residues processed: 48 average time/residue: 0.8454 time to fit residues: 42.5859 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 : 0.328 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 15 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.3129 r_free = 0.3129 target = 0.109775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.093437 restraints weight = 8775.798| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.22 r_work: 0.2792 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7638 Z= 0.137 Angle : 0.503 7.201 10424 Z= 0.252 Chirality : 0.041 0.133 1180 Planarity : 0.004 0.035 1330 Dihedral : 7.756 61.400 1194 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.19 % Allowed : 10.55 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.28), residues: 950 helix: 2.07 (0.24), residues: 488 sheet: 0.26 (0.43), residues: 118 loop : -0.26 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 414 TYR 0.007 0.001 TYR B 777 PHE 0.021 0.002 PHE A 641 TRP 0.005 0.001 TRP B 798 HIS 0.001 0.000 HIS A 603 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 7638) covalent geometry : angle 0.50324 (10424) hydrogen bonds : bond 0.04149 ( 370) hydrogen bonds : angle 4.00188 ( 1044) *********************** 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 54 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.184 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 48 average time/residue: 0.7556 time to fit residues: 37.8837 Evaluate side-chains 52 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 54 optimal weight: 0.1980 chunk 94 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 6 optimal weight: 0.0470 chunk 5 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 overall best weight: 0.9680 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.110440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.094046 restraints weight = 8836.710| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.22 r_work: 0.2803 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1597 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= 0.117 Angle : 0.483 7.200 10424 Z= 0.242 Chirality : 0.041 0.135 1180 Planarity : 0.004 0.034 1330 Dihedral : 7.578 58.987 1194 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.06 % Allowed : 10.69 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.28), residues: 950 helix: 2.12 (0.24), residues: 488 sheet: 0.02 (0.42), residues: 122 loop : -0.17 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 414 TYR 0.007 0.001 TYR B 514 PHE 0.019 0.002 PHE B 641 TRP 0.005 0.001 TRP A 798 HIS 0.001 0.000 HIS B 712 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7638) covalent geometry : angle 0.48347 (10424) hydrogen bonds : bond 0.03869 ( 370) hydrogen bonds : angle 3.94209 ( 1044) *********************** 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 55 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.313 Fit side-chains REVERT: A 800 ASP cc_start: 0.7777 (m-30) cc_final: 0.7514 (t0) REVERT: B 800 ASP cc_start: 0.7782 (m-30) cc_final: 0.7520 (t0) outliers start: 8 outliers final: 6 residues processed: 49 average time/residue: 0.7434 time to fit residues: 38.2783 Evaluate side-chains 53 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 44 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 1 optimal weight: 0.5980 chunk 18 optimal weight: 0.0020 chunk 58 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.6590 ------------------------------------------------------------------------------- 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 = 0.3156 r_free = 0.3156 target = 0.111790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.095409 restraints weight = 8864.537| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.23 r_work: 0.2826 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1634 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= 0.096 Angle : 0.456 7.255 10424 Z= 0.227 Chirality : 0.040 0.136 1180 Planarity : 0.004 0.034 1330 Dihedral : 7.259 54.856 1194 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.28), residues: 950 helix: 2.23 (0.25), residues: 486 sheet: 0.11 (0.43), residues: 122 loop : -0.15 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 414 TYR 0.006 0.001 TYR B 713 PHE 0.018 0.001 PHE B 641 TRP 0.005 0.001 TRP B 798 HIS 0.001 0.000 HIS A 712 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 7638) covalent geometry : angle 0.45644 (10424) hydrogen bonds : bond 0.03445 ( 370) hydrogen bonds : angle 3.83876 ( 1044) *********************** 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 55 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.296 Fit side-chains REVERT: A 800 ASP cc_start: 0.7723 (m-30) cc_final: 0.7520 (t0) REVERT: B 800 ASP cc_start: 0.7747 (m-30) cc_final: 0.7537 (t0) outliers start: 8 outliers final: 6 residues processed: 51 average time/residue: 0.7681 time to fit residues: 40.9116 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 : 0.238 ------------------------------------------------------------------------------- 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 33 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3151 r_free = 0.3151 target = 0.111399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.095092 restraints weight = 8754.660| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.22 r_work: 0.2821 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1634 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= 0.104 Angle : 0.466 7.408 10424 Z= 0.232 Chirality : 0.040 0.136 1180 Planarity : 0.004 0.034 1330 Dihedral : 7.290 56.571 1194 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.19 % Allowed : 10.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.28), residues: 950 helix: 2.24 (0.25), residues: 486 sheet: 0.21 (0.43), residues: 122 loop : -0.15 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 414 TYR 0.006 0.001 TYR A 713 PHE 0.019 0.002 PHE A 641 TRP 0.005 0.001 TRP B 798 HIS 0.001 0.000 HIS B 712 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 7638) covalent geometry : angle 0.46600 (10424) hydrogen bonds : bond 0.03583 ( 370) hydrogen bonds : angle 3.85022 ( 1044) *********************** 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 59 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.203 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 53 average time/residue: 0.7594 time to fit residues: 42.1333 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 : 0.299 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 61 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 chunk 27 optimal weight: 0.6980 chunk 77 optimal weight: 0.3980 chunk 57 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3144 r_free = 0.3144 target = 0.110844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.094640 restraints weight = 8851.522| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 1.21 r_work: 0.2816 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1668 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= 0.113 Angle : 0.483 7.567 10424 Z= 0.243 Chirality : 0.040 0.135 1180 Planarity : 0.004 0.034 1330 Dihedral : 7.349 57.249 1194 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.06 % Allowed : 11.35 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.28), residues: 950 helix: 2.24 (0.25), residues: 486 sheet: 0.24 (0.43), residues: 122 loop : -0.16 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 414 TYR 0.006 0.001 TYR B 713 PHE 0.019 0.002 PHE B 641 TRP 0.009 0.001 TRP A 798 HIS 0.001 0.000 HIS B 712 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 7638) covalent geometry : angle 0.48314 (10424) hydrogen bonds : bond 0.03693 ( 370) hydrogen bonds : angle 3.86274 ( 1044) ********************** 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 54 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.292 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 48 average time/residue: 0.7749 time to fit residues: 38.9283 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 : 0.307 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 32 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 chunk 90 optimal weight: 0.0980 chunk 95 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 35 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 10 optimal weight: 0.0070 chunk 62 optimal weight: 0.8980 overall best weight: 0.4398 ------------------------------------------------------------------------------- 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 = 0.3207 r_free = 0.3207 target = 0.115413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.099713 restraints weight = 8643.214| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.17 r_work: 0.2861 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1734 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= 0.087 Angle : 0.449 7.488 10424 Z= 0.224 Chirality : 0.039 0.137 1180 Planarity : 0.004 0.034 1330 Dihedral : 6.994 52.046 1194 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.79 % Allowed : 11.74 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.28), residues: 950 helix: 2.35 (0.25), residues: 486 sheet: 0.32 (0.44), residues: 122 loop : -0.05 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 414 TYR 0.006 0.001 TYR B 713 PHE 0.016 0.001 PHE B 641 TRP 0.006 0.001 TRP A 798 HIS 0.001 0.000 HIS A 712 Details of bonding type rmsd covalent geometry : bond 0.00193 ( 7638) covalent geometry : angle 0.44863 (10424) hydrogen bonds : bond 0.03130 ( 370) hydrogen bonds : angle 3.73881 ( 1044) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2035.28 seconds wall clock time: 35 minutes 33.91 seconds (2133.91 seconds total)