Starting phenix.real_space_refine on Mon Apr 28 12:07:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k3h_36851/04_2025/8k3h_36851.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3h_36851/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8k3h_36851/04_2025/8k3h_36851.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3h_36851/04_2025/8k3h_36851.map" model { file = "/net/cci-nas-00/data/ceres_data/8k3h_36851/04_2025/8k3h_36851.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3h_36851/04_2025/8k3h_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-5669/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: 4.99, per 1000 atoms: 0.67 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: 1.75 Conformation dependent library (CDL) restraints added in 1.0 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: 0.92 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: 2.23 Time building geometry restraints manager: 2.08 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: 0.04 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: 1.830 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.820 Find NCS groups from input model: 0.140 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:12.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.390 ------------------------------------------------------------------------------- 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 : 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 Details of bonding type rmsd hydrogen bonds : bond 0.24009 ( 370) hydrogen bonds : angle 6.41295 ( 1044) covalent geometry : bond 0.00346 ( 7638) covalent geometry : angle 0.52170 (10424) *********************** 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 : 0.882 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 1.6428 time to fit residues: 117.3422 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 : 0.802 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.111386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.095173 restraints weight = 8721.202| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.22 r_work: 0.2845 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1184 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= 0.123 Angle : 0.502 6.691 10424 Z= 0.256 Chirality : 0.041 0.136 1180 Planarity : 0.004 0.036 1330 Dihedral : 9.704 57.802 1194 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.19 % Allowed : 5.01 % Favored : 93.80 % 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: 1.18 (0.28), residues: 950 helix: 1.59 (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 A 798 HIS 0.003 0.001 HIS B 485 PHE 0.019 0.002 PHE B 641 TYR 0.011 0.001 TYR A 458 ARG 0.002 0.000 ARG A 414 Details of bonding type rmsd hydrogen bonds : bond 0.04796 ( 370) hydrogen bonds : angle 4.50843 ( 1044) covalent geometry : bond 0.00277 ( 7638) covalent geometry : angle 0.50210 (10424) *********************** 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 : 0.880 Fit side-chains REVERT: A 485 HIS cc_start: 0.8783 (p90) cc_final: 0.8525 (p-80) REVERT: B 485 HIS cc_start: 0.8763 (p90) cc_final: 0.8500 (p-80) outliers start: 9 outliers final: 4 residues processed: 60 average time/residue: 1.5654 time to fit residues: 98.8191 Evaluate side-chains 55 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 57 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 0.3980 chunk 39 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 37 optimal weight: 0.3980 chunk 94 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3136 r_free = 0.3136 target = 0.110340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.093991 restraints weight = 8795.784| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.21 r_work: 0.2807 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7638 Z= 0.130 Angle : 0.499 6.692 10424 Z= 0.251 Chirality : 0.041 0.134 1180 Planarity : 0.004 0.036 1330 Dihedral : 8.402 59.572 1194 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.32 % Allowed : 7.92 % Favored : 90.77 % 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: 1.39 (0.28), residues: 950 helix: 1.87 (0.24), residues: 488 sheet: 0.05 (0.43), residues: 122 loop : -0.06 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 798 HIS 0.002 0.001 HIS B 485 PHE 0.020 0.002 PHE A 641 TYR 0.009 0.001 TYR A 458 ARG 0.003 0.000 ARG B 387 Details of bonding type rmsd hydrogen bonds : bond 0.04396 ( 370) hydrogen bonds : angle 4.21029 ( 1044) covalent geometry : bond 0.00303 ( 7638) covalent geometry : angle 0.49937 (10424) *********************** 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 61 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.869 Fit side-chains REVERT: A 367 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.6539 (mp0) REVERT: A 414 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7895 (ptt90) REVERT: B 367 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.6543 (mp0) REVERT: B 414 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8006 (ptt90) outliers start: 10 outliers final: 4 residues processed: 54 average time/residue: 1.4440 time to fit residues: 82.4084 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 : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 414 ARG Chi-restraints excluded: chain B residue 565 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 77 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3101 r_free = 0.3101 target = 0.107806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.091446 restraints weight = 8775.957| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.21 r_work: 0.2779 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7638 Z= 0.196 Angle : 0.565 7.709 10424 Z= 0.285 Chirality : 0.044 0.136 1180 Planarity : 0.005 0.037 1330 Dihedral : 8.779 65.852 1194 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.06 % Allowed : 8.71 % Favored : 90.24 % 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: 1.22 (0.28), residues: 950 helix: 1.77 (0.24), residues: 488 sheet: 0.13 (0.42), residues: 118 loop : -0.27 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 798 HIS 0.002 0.001 HIS B 603 PHE 0.023 0.002 PHE A 641 TYR 0.008 0.002 TYR B 514 ARG 0.004 0.000 ARG B 510 Details of bonding type rmsd hydrogen bonds : bond 0.04958 ( 370) hydrogen bonds : angle 4.26615 ( 1044) covalent geometry : bond 0.00474 ( 7638) covalent geometry : angle 0.56544 (10424) *********************** 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 48 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 414 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8030 (ptt90) REVERT: B 414 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8043 (ptt90) outliers start: 8 outliers final: 6 residues processed: 44 average time/residue: 1.8261 time to fit residues: 84.6467 Evaluate side-chains 48 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 414 ARG 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 43 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3140 r_free = 0.3140 target = 0.110578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.094318 restraints weight = 8712.237| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.22 r_work: 0.2806 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1555 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= 0.112 Angle : 0.481 7.154 10424 Z= 0.242 Chirality : 0.040 0.135 1180 Planarity : 0.004 0.035 1330 Dihedral : 7.828 58.269 1194 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.79 % Allowed : 10.55 % 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: 1.41 (0.28), residues: 950 helix: 1.99 (0.24), residues: 488 sheet: 0.16 (0.42), residues: 118 loop : -0.26 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 798 HIS 0.001 0.000 HIS A 712 PHE 0.018 0.002 PHE A 641 TYR 0.007 0.001 TYR A 514 ARG 0.003 0.000 ARG B 510 Details of bonding type rmsd hydrogen bonds : bond 0.03914 ( 370) hydrogen bonds : angle 4.04544 ( 1044) covalent geometry : bond 0.00260 ( 7638) covalent geometry : angle 0.48081 (10424) *********************** 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 50 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: A 800 ASP cc_start: 0.7847 (m-30) cc_final: 0.7521 (t0) REVERT: B 367 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.6398 (mp0) REVERT: B 800 ASP cc_start: 0.7852 (m-30) cc_final: 0.7524 (t0) outliers start: 6 outliers final: 5 residues processed: 44 average time/residue: 1.7141 time to fit residues: 79.3820 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 : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 367 GLU 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 84 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 79 optimal weight: 0.0770 chunk 30 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 14 optimal weight: 0.2980 chunk 26 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.4342 ------------------------------------------------------------------------------- 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 = 0.3119 r_free = 0.3119 target = 0.109043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.092592 restraints weight = 8763.298| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 1.22 r_work: 0.2783 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7638 Z= 0.152 Angle : 0.520 7.643 10424 Z= 0.260 Chirality : 0.042 0.133 1180 Planarity : 0.004 0.035 1330 Dihedral : 7.986 63.108 1194 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.19 % Allowed : 10.42 % Favored : 88.39 % 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: 1.36 (0.28), residues: 950 helix: 1.96 (0.24), residues: 488 sheet: 0.12 (0.42), residues: 118 loop : -0.30 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 798 HIS 0.001 0.000 HIS A 603 PHE 0.022 0.002 PHE B 641 TYR 0.008 0.001 TYR B 514 ARG 0.005 0.000 ARG A 414 Details of bonding type rmsd hydrogen bonds : bond 0.04368 ( 370) hydrogen bonds : angle 4.08670 ( 1044) covalent geometry : bond 0.00366 ( 7638) covalent geometry : angle 0.51979 (10424) *********************** 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 53 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 47 average time/residue: 1.7757 time to fit residues: 87.7037 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 : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 367 GLU 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 367 GLU 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 8 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 = 0.109233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.092837 restraints weight = 8752.857| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.22 r_work: 0.2787 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1612 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= 0.136 Angle : 0.505 7.495 10424 Z= 0.253 Chirality : 0.041 0.133 1180 Planarity : 0.004 0.035 1330 Dihedral : 7.802 61.906 1194 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.19 % Allowed : 10.42 % Favored : 88.39 % 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: 1.38 (0.28), residues: 950 helix: 1.96 (0.24), residues: 490 sheet: 0.12 (0.41), residues: 118 loop : -0.27 (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 B 536 PHE 0.020 0.002 PHE B 641 TYR 0.008 0.001 TYR A 514 ARG 0.006 0.000 ARG B 414 Details of bonding type rmsd hydrogen bonds : bond 0.04161 ( 370) hydrogen bonds : angle 4.02635 ( 1044) covalent geometry : bond 0.00326 ( 7638) covalent geometry : angle 0.50539 (10424) *********************** 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: 9 poor density : 46 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 800 ASP cc_start: 0.7840 (m-30) cc_final: 0.7517 (t0) REVERT: B 800 ASP cc_start: 0.7846 (m-30) cc_final: 0.7523 (t0) outliers start: 9 outliers final: 8 residues processed: 49 average time/residue: 1.8079 time to fit residues: 93.0161 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 : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 367 GLU 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 367 GLU 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 33 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 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 = 0.3141 r_free = 0.3141 target = 0.110702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.094298 restraints weight = 8864.966| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.23 r_work: 0.2808 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1625 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= 0.106 Angle : 0.473 7.290 10424 Z= 0.237 Chirality : 0.040 0.135 1180 Planarity : 0.004 0.035 1330 Dihedral : 7.480 57.536 1194 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.06 % Allowed : 10.42 % 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 (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: 1.50 (0.28), residues: 950 helix: 2.06 (0.24), residues: 490 sheet: -0.05 (0.41), residues: 122 loop : -0.12 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 798 HIS 0.001 0.000 HIS A 712 PHE 0.018 0.002 PHE B 641 TYR 0.007 0.001 TYR B 514 ARG 0.006 0.000 ARG A 414 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 370) hydrogen bonds : angle 3.92429 ( 1044) covalent geometry : bond 0.00244 ( 7638) covalent geometry : angle 0.47348 (10424) *********************** 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: 8 poor density : 49 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 800 ASP cc_start: 0.7822 (m-30) cc_final: 0.7525 (t0) REVERT: B 800 ASP cc_start: 0.7819 (m-30) cc_final: 0.7529 (t0) outliers start: 8 outliers final: 8 residues processed: 51 average time/residue: 1.7261 time to fit residues: 92.4867 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 : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 367 GLU 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 367 GLU 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 19 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 9 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 42 optimal weight: 0.4980 chunk 64 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.111810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.095489 restraints weight = 8794.010| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.21 r_work: 0.2829 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1651 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= 0.097 Angle : 0.458 7.436 10424 Z= 0.228 Chirality : 0.040 0.135 1180 Planarity : 0.004 0.035 1330 Dihedral : 7.214 54.924 1194 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.06 % Allowed : 10.55 % Favored : 88.39 % 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: 1.64 (0.28), residues: 950 helix: 2.21 (0.25), residues: 488 sheet: 0.09 (0.42), residues: 122 loop : -0.13 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 798 HIS 0.001 0.000 HIS A 712 PHE 0.018 0.001 PHE A 641 TYR 0.007 0.001 TYR B 713 ARG 0.007 0.000 ARG A 414 Details of bonding type rmsd hydrogen bonds : bond 0.03436 ( 370) hydrogen bonds : angle 3.82972 ( 1044) covalent geometry : bond 0.00223 ( 7638) covalent geometry : angle 0.45805 (10424) *********************** 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: 8 poor density : 51 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 53 average time/residue: 1.6843 time to fit residues: 93.9732 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 : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 GLU 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 5 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 663 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.108584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.092190 restraints weight = 8917.924| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 1.22 r_work: 0.2774 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7638 Z= 0.173 Angle : 0.548 7.822 10424 Z= 0.276 Chirality : 0.043 0.137 1180 Planarity : 0.005 0.036 1330 Dihedral : 7.911 64.704 1194 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % 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 (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: 1.43 (0.28), residues: 950 helix: 2.02 (0.24), residues: 488 sheet: 0.29 (0.42), residues: 118 loop : -0.33 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 798 HIS 0.002 0.001 HIS B 536 PHE 0.022 0.002 PHE B 641 TYR 0.008 0.001 TYR B 514 ARG 0.006 0.000 ARG B 414 Details of bonding type rmsd hydrogen bonds : bond 0.04518 ( 370) hydrogen bonds : angle 4.04538 ( 1044) covalent geometry : bond 0.00419 ( 7638) covalent geometry : angle 0.54810 (10424) ********************** 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 50 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 44 average time/residue: 1.7757 time to fit residues: 82.0239 Evaluate side-chains 50 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 367 GLU 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 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 65 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 42 optimal weight: 0.4980 chunk 83 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 35 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.111375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.095145 restraints weight = 8799.605| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.21 r_work: 0.2819 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1688 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= 0.098 Angle : 0.473 7.621 10424 Z= 0.238 Chirality : 0.040 0.134 1180 Planarity : 0.004 0.035 1330 Dihedral : 7.317 55.769 1194 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.79 % Allowed : 11.35 % 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: 1.61 (0.28), residues: 950 helix: 2.18 (0.25), residues: 488 sheet: 0.12 (0.43), residues: 122 loop : -0.17 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 798 HIS 0.001 0.000 HIS A 712 PHE 0.018 0.002 PHE A 641 TYR 0.007 0.001 TYR B 713 ARG 0.006 0.000 ARG B 414 Details of bonding type rmsd hydrogen bonds : bond 0.03528 ( 370) hydrogen bonds : angle 3.86928 ( 1044) covalent geometry : bond 0.00223 ( 7638) covalent geometry : angle 0.47320 (10424) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4246.67 seconds wall clock time: 73 minutes 23.17 seconds (4403.17 seconds total)