Starting phenix.real_space_refine on Sun May 11 20:59:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fr0_29394/05_2025/8fr0_29394.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fr0_29394/05_2025/8fr0_29394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fr0_29394/05_2025/8fr0_29394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fr0_29394/05_2025/8fr0_29394.map" model { file = "/net/cci-nas-00/data/ceres_data/8fr0_29394/05_2025/8fr0_29394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fr0_29394/05_2025/8fr0_29394.cif" } resolution = 3.04 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= 0.003 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 S 64 5.16 5 Cl 4 4.86 5 C 5332 2.51 5 N 1384 2.21 5 O 1608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8392 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "B" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2111 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "D" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2111 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 5.91, per 1000 atoms: 0.70 Number of scatterers: 8392 At special positions: 0 Unit cell: (117.26, 84.46, 85.28, 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) Cl 4 17.00 S 64 16.00 O 1608 8.00 N 1384 7.00 C 5332 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 1.0 seconds 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 19 sheets defined 42.0% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.687A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.566A pdb=" N GLU A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'B' and resid 423 through 436 removed outlier: 3.665A pdb=" N ASP B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 635 through 642 Processing helix chain 'B' and resid 654 through 662 Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 695 Processing helix chain 'B' and resid 706 through 715 Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.658A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 635 through 642 removed outlier: 3.589A pdb=" N LEU C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 661 Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 695 Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'D' and resid 423 through 436 removed outlier: 3.797A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 636 through 642 Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.617A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.523A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 695 Processing helix chain 'D' and resid 706 through 715 Processing helix chain 'D' and resid 742 through 755 Processing helix chain 'D' and resid 758 through 769 removed outlier: 3.602A pdb=" N ASP D 769 " --> pdb=" O LYS D 765 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.427A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA3, first strand: chain 'A' and resid 496 through 498 removed outlier: 4.001A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.505A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 440 through 444 removed outlier: 3.685A pdb=" N ILE B 474 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA7, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AA8, first strand: chain 'B' and resid 496 through 498 removed outlier: 4.075A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.668A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.939A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 395 through 399 removed outlier: 6.328A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 407 through 408 removed outlier: 3.554A pdb=" N GLU C 422 " --> pdb=" O MET C 407 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AB4, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.931A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.411A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 395 through 399 Processing sheet with id=AB7, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB8, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AB9, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.879A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.578A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 327 hydrogen bonds defined for protein. 939 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: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2630 1.35 - 1.48: 2040 1.48 - 1.60: 3724 1.60 - 1.73: 40 1.73 - 1.85: 104 Bond restraints: 8538 Sorted by residual: bond pdb=" C3 CYZ B1302 " pdb=" C4 CYZ B1302 " ideal model delta sigma weight residual 1.334 1.578 -0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C3 CYZ A1302 " pdb=" C4 CYZ A1302 " ideal model delta sigma weight residual 1.334 1.578 -0.244 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C3 CYZ C1302 " pdb=" C4 CYZ C1302 " ideal model delta sigma weight residual 1.334 1.578 -0.244 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C3 CYZ D1302 " pdb=" C4 CYZ D1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C5 CYZ D1302 " pdb=" C6 CYZ D1302 " ideal model delta sigma weight residual 1.553 1.331 0.222 2.00e-02 2.50e+03 1.23e+02 ... (remaining 8533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 11307 1.94 - 3.87: 143 3.87 - 5.81: 30 5.81 - 7.75: 28 7.75 - 9.68: 12 Bond angle restraints: 11520 Sorted by residual: angle pdb=" C9 CYZ D1302 " pdb=" S1 CYZ D1302 " pdb=" N1 CYZ D1302 " ideal model delta sigma weight residual 101.75 111.43 -9.68 3.00e+00 1.11e-01 1.04e+01 angle pdb=" C9 CYZ C1302 " pdb=" S1 CYZ C1302 " pdb=" N1 CYZ C1302 " ideal model delta sigma weight residual 101.75 111.43 -9.68 3.00e+00 1.11e-01 1.04e+01 angle pdb=" C9 CYZ A1302 " pdb=" S1 CYZ A1302 " pdb=" N1 CYZ A1302 " ideal model delta sigma weight residual 101.75 111.36 -9.61 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C9 CYZ B1302 " pdb=" S1 CYZ B1302 " pdb=" N1 CYZ B1302 " ideal model delta sigma weight residual 101.75 111.35 -9.60 3.00e+00 1.11e-01 1.02e+01 angle pdb=" O3 CYZ D1302 " pdb=" S2 CYZ D1302 " pdb=" O4 CYZ D1302 " ideal model delta sigma weight residual 118.35 109.35 9.00 3.00e+00 1.11e-01 9.00e+00 ... (remaining 11515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.59: 4705 22.59 - 45.18: 460 45.18 - 67.77: 57 67.77 - 90.36: 14 90.36 - 112.95: 12 Dihedral angle restraints: 5248 sinusoidal: 2196 harmonic: 3052 Sorted by residual: dihedral pdb=" CB CYS B 718 " pdb=" SG CYS B 718 " pdb=" SG CYS B 773 " pdb=" CB CYS B 773 " ideal model delta sinusoidal sigma weight residual -86.00 -173.62 87.62 1 1.00e+01 1.00e-02 9.20e+01 dihedral pdb=" CB CYS A 718 " pdb=" SG CYS A 718 " pdb=" SG CYS A 773 " pdb=" CB CYS A 773 " ideal model delta sinusoidal sigma weight residual 93.00 175.09 -82.09 1 1.00e+01 1.00e-02 8.28e+01 dihedral pdb=" CB CYS C 718 " pdb=" SG CYS C 718 " pdb=" SG CYS C 773 " pdb=" CB CYS C 773 " ideal model delta sinusoidal sigma weight residual 93.00 152.24 -59.24 1 1.00e+01 1.00e-02 4.69e+01 ... (remaining 5245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1187 0.088 - 0.176: 81 0.176 - 0.263: 0 0.263 - 0.351: 0 0.351 - 0.439: 16 Chirality restraints: 1284 Sorted by residual: chirality pdb=" C8 CYZ A1302 " pdb=" C1 CYZ A1302 " pdb=" N1 CYZ A1302 " pdb=" N2 CYZ A1302 " both_signs ideal model delta sigma weight residual False 2.20 2.64 -0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" C8 CYZ C1302 " pdb=" C1 CYZ C1302 " pdb=" N1 CYZ C1302 " pdb=" N2 CYZ C1302 " both_signs ideal model delta sigma weight residual False 2.20 2.64 -0.44 2.00e-01 2.50e+01 4.79e+00 chirality pdb=" C8 CYZ D1302 " pdb=" C1 CYZ D1302 " pdb=" N1 CYZ D1302 " pdb=" N2 CYZ D1302 " both_signs ideal model delta sigma weight residual False 2.20 2.63 -0.43 2.00e-01 2.50e+01 4.64e+00 ... (remaining 1281 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 736 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO B 737 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 737 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 737 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 493 " -0.025 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO B 494 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 494 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 494 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 736 " 0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO C 737 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 737 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 737 " 0.021 5.00e-02 4.00e+02 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1390 2.76 - 3.30: 7782 3.30 - 3.83: 14394 3.83 - 4.37: 17050 4.37 - 4.90: 29102 Nonbonded interactions: 69718 Sorted by model distance: nonbonded pdb=" O VAL B 681 " pdb=" OH TYR B 700 " model vdw 2.230 3.040 nonbonded pdb=" OH TYR C 424 " pdb=" O HOH C1401 " model vdw 2.262 3.040 nonbonded pdb=" OH TYR A 424 " pdb=" O HOH A1401 " model vdw 2.269 3.040 nonbonded pdb=" OG SER D 654 " pdb=" O HOH D1401 " model vdw 2.279 3.040 nonbonded pdb=" NZ LYS C 409 " pdb=" O GLU C 419 " model vdw 2.286 3.120 ... (remaining 69713 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'B' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 773 or resid 1301 or resid 1302)) selection = (chain 'C' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'D' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 773 or resid 1301 or resid 1302)) } 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: 2.650 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.750 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 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 : 0.015 0.244 8542 Z= 0.725 Angle : 0.691 9.682 11528 Z= 0.300 Chirality : 0.062 0.439 1284 Planarity : 0.004 0.044 1422 Dihedral : 17.612 112.952 3288 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.68 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 21.25 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.10 (0.26), residues: 1044 helix: 1.22 (0.26), residues: 418 sheet: -0.61 (0.36), residues: 170 loop : -1.02 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 766 HIS 0.003 0.001 HIS C 412 PHE 0.008 0.001 PHE C 658 TYR 0.014 0.001 TYR D 673 ARG 0.009 0.001 ARG C 684 Details of bonding type rmsd hydrogen bonds : bond 0.16627 ( 327) hydrogen bonds : angle 6.56348 ( 939) SS BOND : bond 0.00057 ( 4) SS BOND : angle 0.28545 ( 8) covalent geometry : bond 0.01452 ( 8538) covalent geometry : angle 0.69134 (11520) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.971 Fit side-chains REVERT: A 647 TYR cc_start: 0.7876 (p90) cc_final: 0.7449 (p90) REVERT: B 651 ASP cc_start: 0.7706 (t0) cc_final: 0.7061 (t70) REVERT: D 634 GLU cc_start: 0.6781 (mm-30) cc_final: 0.6344 (tm-30) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2817 time to fit residues: 49.0280 Evaluate side-chains 126 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.156122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.131443 restraints weight = 10242.857| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.00 r_work: 0.3406 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8542 Z= 0.122 Angle : 0.504 6.824 11528 Z= 0.251 Chirality : 0.043 0.154 1284 Planarity : 0.004 0.038 1422 Dihedral : 9.777 92.724 1266 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.82 % Favored : 97.99 % Rotamer: Outliers : 2.01 % Allowed : 19.57 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.06 (0.27), residues: 1044 helix: 1.19 (0.26), residues: 434 sheet: -0.49 (0.37), residues: 172 loop : -1.06 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 671 HIS 0.004 0.001 HIS C 412 PHE 0.012 0.001 PHE D 495 TYR 0.017 0.001 TYR D 711 ARG 0.005 0.000 ARG C 684 Details of bonding type rmsd hydrogen bonds : bond 0.03209 ( 327) hydrogen bonds : angle 4.99424 ( 939) SS BOND : bond 0.00085 ( 4) SS BOND : angle 0.32048 ( 8) covalent geometry : bond 0.00289 ( 8538) covalent geometry : angle 0.50402 (11520) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.977 Fit side-chains REVERT: A 633 ILE cc_start: 0.7000 (OUTLIER) cc_final: 0.6654 (pt) REVERT: A 647 TYR cc_start: 0.8014 (p90) cc_final: 0.7515 (p90) REVERT: D 438 PHE cc_start: 0.6383 (p90) cc_final: 0.6044 (p90) outliers start: 18 outliers final: 8 residues processed: 145 average time/residue: 0.2994 time to fit residues: 54.4973 Evaluate side-chains 132 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 765 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 7 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 714 GLN D 764 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.150556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.125532 restraints weight = 10534.160| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.00 r_work: 0.3307 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8542 Z= 0.215 Angle : 0.594 8.014 11528 Z= 0.295 Chirality : 0.047 0.188 1284 Planarity : 0.004 0.032 1422 Dihedral : 9.796 87.266 1266 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.20 % Favored : 97.61 % Rotamer: Outliers : 3.02 % Allowed : 19.35 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.46 (0.26), residues: 1044 helix: 0.85 (0.26), residues: 436 sheet: -0.88 (0.38), residues: 160 loop : -1.20 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 671 HIS 0.004 0.001 HIS B 435 PHE 0.015 0.002 PHE B 659 TYR 0.017 0.002 TYR D 711 ARG 0.006 0.001 ARG C 684 Details of bonding type rmsd hydrogen bonds : bond 0.03955 ( 327) hydrogen bonds : angle 4.85870 ( 939) SS BOND : bond 0.00206 ( 4) SS BOND : angle 0.73605 ( 8) covalent geometry : bond 0.00526 ( 8538) covalent geometry : angle 0.59356 (11520) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.980 Fit side-chains REVERT: B 459 ILE cc_start: 0.8148 (mm) cc_final: 0.7942 (mt) REVERT: B 765 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8104 (tttt) REVERT: D 438 PHE cc_start: 0.6509 (p90) cc_final: 0.6243 (p90) REVERT: D 765 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7825 (tttt) outliers start: 27 outliers final: 15 residues processed: 152 average time/residue: 0.2723 time to fit residues: 53.0429 Evaluate side-chains 139 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 765 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 74 optimal weight: 0.7980 chunk 39 optimal weight: 0.0970 chunk 96 optimal weight: 0.2980 chunk 14 optimal weight: 0.0870 chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 49 optimal weight: 0.0070 chunk 43 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 overall best weight: 0.2374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 714 GLN D 764 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.155212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.130647 restraints weight = 10387.259| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.00 r_work: 0.3396 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8542 Z= 0.086 Angle : 0.477 7.052 11528 Z= 0.236 Chirality : 0.042 0.179 1284 Planarity : 0.003 0.043 1422 Dihedral : 8.715 80.372 1266 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.13 % Allowed : 21.36 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.15 (0.26), residues: 1044 helix: 1.17 (0.27), residues: 436 sheet: -0.80 (0.38), residues: 160 loop : -1.07 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 766 HIS 0.002 0.000 HIS C 412 PHE 0.010 0.001 PHE D 495 TYR 0.012 0.001 TYR D 711 ARG 0.006 0.000 ARG C 684 Details of bonding type rmsd hydrogen bonds : bond 0.02566 ( 327) hydrogen bonds : angle 4.63449 ( 939) SS BOND : bond 0.00071 ( 4) SS BOND : angle 0.25244 ( 8) covalent geometry : bond 0.00191 ( 8538) covalent geometry : angle 0.47758 (11520) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.891 Fit side-chains REVERT: A 647 TYR cc_start: 0.8068 (p90) cc_final: 0.7687 (p90) REVERT: D 438 PHE cc_start: 0.6428 (p90) cc_final: 0.6096 (p90) outliers start: 19 outliers final: 11 residues processed: 144 average time/residue: 0.2586 time to fit residues: 48.1095 Evaluate side-chains 138 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 765 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 78 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 32 optimal weight: 0.2980 chunk 64 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 714 GLN D 764 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.153599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.128867 restraints weight = 10486.905| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.01 r_work: 0.3373 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8542 Z= 0.110 Angle : 0.487 7.052 11528 Z= 0.240 Chirality : 0.043 0.213 1284 Planarity : 0.003 0.041 1422 Dihedral : 7.706 68.896 1266 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.02 % Allowed : 19.80 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.08 (0.26), residues: 1044 helix: 1.22 (0.27), residues: 436 sheet: -0.66 (0.36), residues: 174 loop : -1.08 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 671 HIS 0.001 0.000 HIS B 435 PHE 0.009 0.001 PHE D 495 TYR 0.015 0.001 TYR D 711 ARG 0.006 0.000 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.02813 ( 327) hydrogen bonds : angle 4.58184 ( 939) SS BOND : bond 0.00106 ( 4) SS BOND : angle 0.33494 ( 8) covalent geometry : bond 0.00263 ( 8538) covalent geometry : angle 0.48750 (11520) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 1.013 Fit side-chains REVERT: A 647 TYR cc_start: 0.8084 (p90) cc_final: 0.7745 (p90) REVERT: B 756 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.6776 (mt0) REVERT: C 408 MET cc_start: 0.8029 (tpp) cc_final: 0.7768 (tpp) REVERT: D 438 PHE cc_start: 0.6472 (p90) cc_final: 0.6223 (p90) REVERT: D 647 TYR cc_start: 0.8897 (p90) cc_final: 0.8694 (p90) REVERT: D 673 TYR cc_start: 0.7950 (t80) cc_final: 0.7654 (t80) outliers start: 27 outliers final: 19 residues processed: 154 average time/residue: 0.2756 time to fit residues: 55.5849 Evaluate side-chains 147 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 765 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 15 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 0.0870 chunk 46 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 overall best weight: 1.2762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 764 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.151782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.126640 restraints weight = 10377.977| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.02 r_work: 0.3341 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8542 Z= 0.148 Angle : 0.521 6.794 11528 Z= 0.258 Chirality : 0.045 0.220 1284 Planarity : 0.004 0.041 1422 Dihedral : 7.273 58.068 1266 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.91 % Allowed : 20.69 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.19 (0.26), residues: 1044 helix: 1.16 (0.27), residues: 436 sheet: -0.87 (0.38), residues: 160 loop : -1.09 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 671 HIS 0.002 0.001 HIS B 435 PHE 0.011 0.002 PHE A 495 TYR 0.016 0.002 TYR D 711 ARG 0.006 0.000 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.03077 ( 327) hydrogen bonds : angle 4.58584 ( 939) SS BOND : bond 0.00146 ( 4) SS BOND : angle 0.56656 ( 8) covalent geometry : bond 0.00359 ( 8538) covalent geometry : angle 0.52112 (11520) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.905 Fit side-chains REVERT: A 647 TYR cc_start: 0.8120 (p90) cc_final: 0.7767 (p90) REVERT: B 756 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.6745 (mt0) REVERT: B 765 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8156 (tttt) REVERT: C 407 MET cc_start: 0.8040 (mpp) cc_final: 0.7650 (mtt) REVERT: D 438 PHE cc_start: 0.6450 (p90) cc_final: 0.6240 (p90) REVERT: D 647 TYR cc_start: 0.8926 (p90) cc_final: 0.8679 (p90) REVERT: D 673 TYR cc_start: 0.7996 (t80) cc_final: 0.7624 (t80) REVERT: D 765 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7861 (tttt) outliers start: 26 outliers final: 20 residues processed: 159 average time/residue: 0.2848 time to fit residues: 57.1760 Evaluate side-chains 153 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 765 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 101 optimal weight: 0.0030 chunk 37 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 764 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.151741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.126652 restraints weight = 10526.175| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.04 r_work: 0.3341 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8542 Z= 0.134 Angle : 0.507 6.447 11528 Z= 0.252 Chirality : 0.045 0.220 1284 Planarity : 0.003 0.042 1422 Dihedral : 6.927 55.075 1266 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.02 % Allowed : 20.81 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.16 (0.26), residues: 1044 helix: 1.19 (0.26), residues: 436 sheet: -0.90 (0.38), residues: 160 loop : -1.07 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 671 HIS 0.002 0.001 HIS B 435 PHE 0.009 0.001 PHE B 659 TYR 0.017 0.001 TYR D 711 ARG 0.006 0.001 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.02967 ( 327) hydrogen bonds : angle 4.55788 ( 939) SS BOND : bond 0.00143 ( 4) SS BOND : angle 0.46965 ( 8) covalent geometry : bond 0.00325 ( 8538) covalent geometry : angle 0.50701 (11520) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.987 Fit side-chains REVERT: A 647 TYR cc_start: 0.8120 (p90) cc_final: 0.7804 (p90) REVERT: B 756 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.6723 (mt0) REVERT: B 765 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8209 (tttt) REVERT: C 407 MET cc_start: 0.8023 (mpp) cc_final: 0.7657 (mtt) REVERT: D 438 PHE cc_start: 0.6456 (p90) cc_final: 0.6256 (p90) REVERT: D 647 TYR cc_start: 0.8915 (p90) cc_final: 0.8672 (p90) REVERT: D 673 TYR cc_start: 0.8017 (t80) cc_final: 0.7653 (t80) outliers start: 27 outliers final: 22 residues processed: 154 average time/residue: 0.2663 time to fit residues: 52.7476 Evaluate side-chains 152 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 765 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 47 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 764 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.151452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.126494 restraints weight = 10536.492| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.02 r_work: 0.3343 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8542 Z= 0.131 Angle : 0.502 6.505 11528 Z= 0.249 Chirality : 0.044 0.200 1284 Planarity : 0.003 0.043 1422 Dihedral : 6.620 51.668 1266 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.24 % Allowed : 20.69 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.14 (0.26), residues: 1044 helix: 1.22 (0.26), residues: 436 sheet: -0.88 (0.38), residues: 160 loop : -1.07 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 671 HIS 0.003 0.001 HIS C 412 PHE 0.009 0.001 PHE D 659 TYR 0.017 0.001 TYR D 711 ARG 0.008 0.001 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.02939 ( 327) hydrogen bonds : angle 4.54737 ( 939) SS BOND : bond 0.00132 ( 4) SS BOND : angle 0.44671 ( 8) covalent geometry : bond 0.00318 ( 8538) covalent geometry : angle 0.50196 (11520) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.989 Fit side-chains REVERT: A 647 TYR cc_start: 0.8120 (p90) cc_final: 0.7828 (p90) REVERT: B 756 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.6713 (mt0) REVERT: B 765 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8240 (tttt) REVERT: D 673 TYR cc_start: 0.8000 (t80) cc_final: 0.7654 (t80) outliers start: 29 outliers final: 23 residues processed: 157 average time/residue: 0.2738 time to fit residues: 55.2995 Evaluate side-chains 155 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 765 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 0.2980 chunk 31 optimal weight: 0.0040 chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 764 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.153800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.129280 restraints weight = 10501.207| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.00 r_work: 0.3377 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8542 Z= 0.096 Angle : 0.471 6.521 11528 Z= 0.235 Chirality : 0.043 0.181 1284 Planarity : 0.003 0.044 1422 Dihedral : 6.166 48.637 1266 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.68 % Allowed : 21.14 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.06 (0.26), residues: 1044 helix: 1.33 (0.26), residues: 436 sheet: -0.93 (0.38), residues: 162 loop : -1.03 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 671 HIS 0.002 0.001 HIS C 412 PHE 0.008 0.001 PHE D 438 TYR 0.017 0.001 TYR D 711 ARG 0.009 0.001 ARG C 684 Details of bonding type rmsd hydrogen bonds : bond 0.02562 ( 327) hydrogen bonds : angle 4.49126 ( 939) SS BOND : bond 0.00088 ( 4) SS BOND : angle 0.26135 ( 8) covalent geometry : bond 0.00225 ( 8538) covalent geometry : angle 0.47102 (11520) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.921 Fit side-chains REVERT: A 647 TYR cc_start: 0.8082 (p90) cc_final: 0.7810 (p90) REVERT: B 756 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.6754 (mt0) REVERT: C 408 MET cc_start: 0.8506 (tpp) cc_final: 0.8257 (mmt) REVERT: D 756 GLN cc_start: 0.4957 (mp-120) cc_final: 0.4618 (mp-120) outliers start: 24 outliers final: 21 residues processed: 157 average time/residue: 0.2747 time to fit residues: 55.1092 Evaluate side-chains 151 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 765 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 43 optimal weight: 4.9990 chunk 52 optimal weight: 0.0770 chunk 60 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 764 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.152842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.128254 restraints weight = 10433.167| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.01 r_work: 0.3365 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8542 Z= 0.109 Angle : 0.485 6.490 11528 Z= 0.241 Chirality : 0.043 0.168 1284 Planarity : 0.003 0.045 1422 Dihedral : 6.006 47.890 1266 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.57 % Allowed : 21.14 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.07 (0.26), residues: 1044 helix: 1.32 (0.26), residues: 436 sheet: -0.95 (0.38), residues: 162 loop : -1.03 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 671 HIS 0.002 0.001 HIS C 412 PHE 0.008 0.001 PHE D 495 TYR 0.018 0.001 TYR D 711 ARG 0.009 0.001 ARG C 684 Details of bonding type rmsd hydrogen bonds : bond 0.02704 ( 327) hydrogen bonds : angle 4.48885 ( 939) SS BOND : bond 0.00114 ( 4) SS BOND : angle 0.36171 ( 8) covalent geometry : bond 0.00261 ( 8538) covalent geometry : angle 0.48494 (11520) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.895 Fit side-chains REVERT: A 647 TYR cc_start: 0.8084 (p90) cc_final: 0.7811 (p90) REVERT: B 756 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.6780 (mt0) REVERT: C 408 MET cc_start: 0.8515 (tpp) cc_final: 0.8268 (mmt) REVERT: D 756 GLN cc_start: 0.5069 (mp-120) cc_final: 0.4677 (mp-120) outliers start: 23 outliers final: 22 residues processed: 149 average time/residue: 0.2679 time to fit residues: 51.3212 Evaluate side-chains 153 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 718 CYS Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 765 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 18 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 764 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.152435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.127753 restraints weight = 10596.750| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.01 r_work: 0.3356 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8542 Z= 0.115 Angle : 0.489 6.463 11528 Z= 0.243 Chirality : 0.043 0.166 1284 Planarity : 0.004 0.045 1422 Dihedral : 6.014 48.109 1266 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.57 % Allowed : 21.25 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.08 (0.26), residues: 1044 helix: 1.31 (0.26), residues: 436 sheet: -0.94 (0.39), residues: 162 loop : -1.05 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 671 HIS 0.001 0.001 HIS C 412 PHE 0.009 0.001 PHE C 495 TYR 0.018 0.001 TYR D 711 ARG 0.008 0.001 ARG C 684 Details of bonding type rmsd hydrogen bonds : bond 0.02740 ( 327) hydrogen bonds : angle 4.48968 ( 939) SS BOND : bond 0.00120 ( 4) SS BOND : angle 0.37943 ( 8) covalent geometry : bond 0.00277 ( 8538) covalent geometry : angle 0.48908 (11520) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4462.72 seconds wall clock time: 78 minutes 12.10 seconds (4692.10 seconds total)