Starting phenix.real_space_refine on Fri Aug 22 22:51:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fr0_29394/08_2025/8fr0_29394.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fr0_29394/08_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_29394/08_2025/8fr0_29394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fr0_29394/08_2025/8fr0_29394.map" model { file = "/net/cci-nas-00/data/ceres_data/8fr0_29394/08_2025/8fr0_29394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fr0_29394/08_2025/8fr0_29394.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.90, per 1000 atoms: 0.23 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: 0.53 Conformation dependent library (CDL) restraints added in 325.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.20 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: 0.91 Time building geometry restraints manager: 0.70 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 773 or resid 1301 through 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 1302)) selection = (chain 'C' and (resid 393 through 773 or resid 1301 through 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 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: 3.390 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.740 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.820 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (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 ARG 0.009 0.001 ARG C 684 TYR 0.014 0.001 TYR D 673 PHE 0.008 0.001 PHE C 658 TRP 0.012 0.001 TRP D 766 HIS 0.003 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.01452 ( 8538) covalent geometry : angle 0.69134 (11520) SS BOND : bond 0.00057 ( 4) SS BOND : angle 0.28545 ( 8) hydrogen bonds : bond 0.16627 ( 327) hydrogen bonds : angle 6.56348 ( 939) *********************** 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 : 0.265 Fit side-chains REVERT: A 647 TYR cc_start: 0.7876 (p90) cc_final: 0.7450 (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: 0.1245 time to fit residues: 21.7194 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 : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.0570 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.7700 ------------------------------------------------------------------------------- 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 = 0.3821 r_free = 0.3821 target = 0.156368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.131572 restraints weight = 10341.167| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.03 r_work: 0.3406 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8542 Z= 0.113 Angle : 0.498 6.976 11528 Z= 0.247 Chirality : 0.043 0.161 1284 Planarity : 0.004 0.038 1422 Dihedral : 9.644 90.940 1266 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.82 % Favored : 97.99 % Rotamer: Outliers : 2.01 % Allowed : 19.46 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.27), residues: 1044 helix: 1.20 (0.26), residues: 434 sheet: -0.48 (0.37), residues: 172 loop : -1.05 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 684 TYR 0.016 0.001 TYR D 711 PHE 0.012 0.001 PHE D 495 TRP 0.012 0.001 TRP B 671 HIS 0.003 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8538) covalent geometry : angle 0.49809 (11520) SS BOND : bond 0.00077 ( 4) SS BOND : angle 0.29971 ( 8) hydrogen bonds : bond 0.03136 ( 327) hydrogen bonds : angle 4.95666 ( 939) *********************** 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 152 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.250 Fit side-chains REVERT: A 407 MET cc_start: 0.7894 (mpp) cc_final: 0.7156 (mtt) REVERT: A 633 ILE cc_start: 0.7053 (OUTLIER) cc_final: 0.6700 (pt) REVERT: A 647 TYR cc_start: 0.8037 (p90) cc_final: 0.7552 (p90) REVERT: D 402 GLU cc_start: 0.7524 (tp30) cc_final: 0.7309 (mm-30) REVERT: D 438 PHE cc_start: 0.6387 (p90) cc_final: 0.6038 (p90) outliers start: 18 outliers final: 9 residues processed: 146 average time/residue: 0.1214 time to fit residues: 22.4796 Evaluate side-chains 133 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 497 SER 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 81 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 40 optimal weight: 0.4980 chunk 75 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 100 optimal weight: 8.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.155440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.130686 restraints weight = 10325.801| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.02 r_work: 0.3391 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8542 Z= 0.107 Angle : 0.482 7.175 11528 Z= 0.238 Chirality : 0.043 0.181 1284 Planarity : 0.003 0.034 1422 Dihedral : 8.748 79.994 1266 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.01 % Favored : 97.89 % Rotamer: Outliers : 2.35 % Allowed : 19.35 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.26), residues: 1044 helix: 1.22 (0.26), residues: 436 sheet: -0.47 (0.37), residues: 172 loop : -1.08 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 684 TYR 0.014 0.001 TYR D 711 PHE 0.011 0.001 PHE D 495 TRP 0.008 0.001 TRP B 671 HIS 0.002 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 8538) covalent geometry : angle 0.48220 (11520) SS BOND : bond 0.00111 ( 4) SS BOND : angle 0.36084 ( 8) hydrogen bonds : bond 0.02926 ( 327) hydrogen bonds : angle 4.71474 ( 939) *********************** 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 149 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.261 Fit side-chains REVERT: A 633 ILE cc_start: 0.7069 (OUTLIER) cc_final: 0.6717 (pt) REVERT: A 647 TYR cc_start: 0.8035 (p90) cc_final: 0.7657 (p90) REVERT: D 402 GLU cc_start: 0.7572 (tp30) cc_final: 0.7361 (mm-30) REVERT: D 438 PHE cc_start: 0.6449 (p90) cc_final: 0.6198 (p90) outliers start: 21 outliers final: 12 residues processed: 146 average time/residue: 0.1115 time to fit residues: 20.9724 Evaluate side-chains 134 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 633 ILE 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 498 LEU Chi-restraints excluded: chain B residue 748 LEU 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 498 LEU 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 21 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 105 optimal weight: 0.3980 chunk 7 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 764 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.151517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.126228 restraints weight = 10619.063| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.04 r_work: 0.3335 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8542 Z= 0.160 Angle : 0.532 7.064 11528 Z= 0.262 Chirality : 0.045 0.212 1284 Planarity : 0.003 0.037 1422 Dihedral : 8.077 69.348 1266 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.91 % Allowed : 19.02 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.26), residues: 1044 helix: 1.14 (0.26), residues: 436 sheet: -0.82 (0.38), residues: 160 loop : -1.08 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 684 TYR 0.016 0.002 TYR D 711 PHE 0.012 0.002 PHE D 495 TRP 0.010 0.001 TRP B 671 HIS 0.002 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 8538) covalent geometry : angle 0.53201 (11520) SS BOND : bond 0.00167 ( 4) SS BOND : angle 0.49923 ( 8) hydrogen bonds : bond 0.03301 ( 327) hydrogen bonds : angle 4.67018 ( 939) *********************** 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 159 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.259 Fit side-chains REVERT: A 647 TYR cc_start: 0.8078 (p90) cc_final: 0.7682 (p90) REVERT: B 660 ARG cc_start: 0.8734 (ttm-80) cc_final: 0.8477 (ttp-170) REVERT: B 756 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.6769 (mt0) REVERT: B 765 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8119 (tttt) REVERT: D 402 GLU cc_start: 0.7566 (tp30) cc_final: 0.7288 (mm-30) REVERT: D 438 PHE cc_start: 0.6450 (p90) cc_final: 0.6219 (p90) REVERT: D 647 TYR cc_start: 0.8921 (p90) cc_final: 0.8720 (p90) REVERT: D 765 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7785 (tttt) outliers start: 26 outliers final: 14 residues processed: 155 average time/residue: 0.1078 time to fit residues: 21.4779 Evaluate side-chains 145 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 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 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 765 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 41 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 39 optimal weight: 0.0040 chunk 22 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.154150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.129211 restraints weight = 10552.726| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.04 r_work: 0.3375 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1533 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= 0.099 Angle : 0.470 6.619 11528 Z= 0.233 Chirality : 0.043 0.206 1284 Planarity : 0.003 0.039 1422 Dihedral : 7.170 59.389 1266 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.46 % Allowed : 20.02 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.26), residues: 1044 helix: 1.25 (0.27), residues: 436 sheet: -0.79 (0.38), residues: 160 loop : -1.01 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 684 TYR 0.015 0.001 TYR D 711 PHE 0.009 0.001 PHE D 495 TRP 0.007 0.001 TRP A 766 HIS 0.001 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 8538) covalent geometry : angle 0.46969 (11520) SS BOND : bond 0.00095 ( 4) SS BOND : angle 0.25736 ( 8) hydrogen bonds : bond 0.02676 ( 327) hydrogen bonds : angle 4.58923 ( 939) *********************** 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 158 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.247 Fit side-chains REVERT: A 647 TYR cc_start: 0.8066 (p90) cc_final: 0.7719 (p90) REVERT: D 438 PHE cc_start: 0.6425 (p90) cc_final: 0.6204 (p90) outliers start: 22 outliers final: 15 residues processed: 152 average time/residue: 0.1074 time to fit residues: 20.8878 Evaluate side-chains 146 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 442 LEU 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 C residue 666 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 765 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 72 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 92 optimal weight: 0.0570 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 0.0170 chunk 43 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.154945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.130107 restraints weight = 10509.854| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.04 r_work: 0.3389 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1637 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= 0.093 Angle : 0.459 6.476 11528 Z= 0.230 Chirality : 0.043 0.203 1284 Planarity : 0.003 0.041 1422 Dihedral : 6.466 53.483 1266 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.57 % Allowed : 20.13 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.26), residues: 1044 helix: 1.34 (0.27), residues: 436 sheet: -0.85 (0.38), residues: 162 loop : -1.02 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 684 TYR 0.016 0.001 TYR D 711 PHE 0.008 0.001 PHE D 495 TRP 0.007 0.001 TRP A 766 HIS 0.001 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 8538) covalent geometry : angle 0.45957 (11520) SS BOND : bond 0.00082 ( 4) SS BOND : angle 0.29650 ( 8) hydrogen bonds : bond 0.02552 ( 327) hydrogen bonds : angle 4.52700 ( 939) *********************** 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 157 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.200 Fit side-chains REVERT: A 647 TYR cc_start: 0.8065 (p90) cc_final: 0.7759 (p90) REVERT: B 756 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.6759 (mt0) REVERT: C 408 MET cc_start: 0.7978 (tpp) cc_final: 0.7696 (tpp) REVERT: D 438 PHE cc_start: 0.6397 (p90) cc_final: 0.6196 (p90) REVERT: D 629 MET cc_start: 0.6535 (tpt) cc_final: 0.6287 (tpt) REVERT: D 673 TYR cc_start: 0.7927 (t80) cc_final: 0.7668 (t80) outliers start: 23 outliers final: 17 residues processed: 152 average time/residue: 0.1137 time to fit residues: 22.2915 Evaluate side-chains 147 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 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 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 765 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 12 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 63 optimal weight: 0.0670 chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 91 optimal weight: 0.0980 overall best weight: 0.6120 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.154490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.129788 restraints weight = 10561.219| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.03 r_work: 0.3380 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 : 0.002 0.023 8542 Z= 0.098 Angle : 0.462 6.479 11528 Z= 0.232 Chirality : 0.043 0.198 1284 Planarity : 0.003 0.042 1422 Dihedral : 6.087 48.578 1266 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.57 % Allowed : 20.47 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.26), residues: 1044 helix: 1.34 (0.26), residues: 436 sheet: -0.86 (0.38), residues: 162 loop : -0.97 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 684 TYR 0.016 0.001 TYR D 711 PHE 0.008 0.001 PHE D 495 TRP 0.006 0.001 TRP D 671 HIS 0.001 0.000 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 8538) covalent geometry : angle 0.46218 (11520) SS BOND : bond 0.00093 ( 4) SS BOND : angle 0.33533 ( 8) hydrogen bonds : bond 0.02573 ( 327) hydrogen bonds : angle 4.51044 ( 939) *********************** 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 153 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.343 Fit side-chains REVERT: A 647 TYR cc_start: 0.8063 (p90) cc_final: 0.7783 (p90) REVERT: B 756 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.6780 (mt0) REVERT: B 765 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8178 (tttt) REVERT: C 408 MET cc_start: 0.7956 (tpp) cc_final: 0.7701 (tpp) REVERT: D 673 TYR cc_start: 0.7925 (t80) cc_final: 0.7706 (t80) outliers start: 23 outliers final: 18 residues processed: 148 average time/residue: 0.1170 time to fit residues: 22.2605 Evaluate side-chains 150 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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 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 718 CYS 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 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 765 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 48 optimal weight: 0.0270 chunk 31 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 2 optimal weight: 0.0570 chunk 86 optimal weight: 1.9990 chunk 28 optimal weight: 0.0070 overall best weight: 0.3574 ------------------------------------------------------------------------------- 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 = 0.3821 r_free = 0.3821 target = 0.156185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.131862 restraints weight = 10415.537| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.01 r_work: 0.3410 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8542 Z= 0.084 Angle : 0.440 6.486 11528 Z= 0.222 Chirality : 0.042 0.179 1284 Planarity : 0.003 0.042 1422 Dihedral : 5.646 45.103 1266 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.24 % Allowed : 21.03 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.26), residues: 1044 helix: 1.43 (0.26), residues: 436 sheet: -0.84 (0.38), residues: 162 loop : -0.93 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 684 TYR 0.016 0.001 TYR D 711 PHE 0.008 0.001 PHE D 438 TRP 0.007 0.001 TRP A 766 HIS 0.001 0.000 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00192 ( 8538) covalent geometry : angle 0.43990 (11520) SS BOND : bond 0.00072 ( 4) SS BOND : angle 0.24458 ( 8) hydrogen bonds : bond 0.02337 ( 327) hydrogen bonds : angle 4.49820 ( 939) *********************** 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 156 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.385 Fit side-chains REVERT: A 647 TYR cc_start: 0.8048 (p90) cc_final: 0.7805 (p90) REVERT: A 714 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.6901 (mp10) REVERT: B 756 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.6743 (mt0) REVERT: B 765 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8152 (tttt) REVERT: C 407 MET cc_start: 0.8304 (mpp) cc_final: 0.7579 (mtt) REVERT: D 760 ASP cc_start: 0.7285 (m-30) cc_final: 0.6988 (m-30) outliers start: 20 outliers final: 16 residues processed: 151 average time/residue: 0.1328 time to fit residues: 25.6536 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 : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 714 GLN 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 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 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 D residue 399 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 20 optimal weight: 0.0770 chunk 74 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.9540 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.153198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.128422 restraints weight = 10530.043| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.02 r_work: 0.3365 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1799 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= 0.122 Angle : 0.477 6.118 11528 Z= 0.241 Chirality : 0.043 0.166 1284 Planarity : 0.004 0.044 1422 Dihedral : 5.834 46.906 1266 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.35 % Allowed : 21.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.26), residues: 1044 helix: 1.33 (0.26), residues: 436 sheet: -0.86 (0.38), residues: 162 loop : -0.97 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 684 TYR 0.017 0.001 TYR D 711 PHE 0.009 0.001 PHE D 659 TRP 0.007 0.001 TRP B 671 HIS 0.002 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8538) covalent geometry : angle 0.47690 (11520) SS BOND : bond 0.00118 ( 4) SS BOND : angle 0.41061 ( 8) hydrogen bonds : bond 0.02772 ( 327) hydrogen bonds : angle 4.51599 ( 939) *********************** 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 152 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.352 Fit side-chains REVERT: A 647 TYR cc_start: 0.8062 (p90) cc_final: 0.7773 (p90) REVERT: B 756 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.6743 (mt0) REVERT: B 765 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8187 (tttt) REVERT: C 407 MET cc_start: 0.8277 (mpp) cc_final: 0.7565 (mtt) REVERT: C 408 MET cc_start: 0.8004 (tpp) cc_final: 0.7647 (tpp) outliers start: 21 outliers final: 19 residues processed: 148 average time/residue: 0.1353 time to fit residues: 25.5699 Evaluate side-chains 148 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 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 718 CYS 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 D residue 399 THR 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 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 41 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 0.0050 chunk 101 optimal weight: 0.0060 chunk 12 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.9614 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.152922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.128217 restraints weight = 10558.618| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.01 r_work: 0.3363 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1888 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= 0.121 Angle : 0.477 6.049 11528 Z= 0.241 Chirality : 0.043 0.164 1284 Planarity : 0.004 0.045 1422 Dihedral : 5.953 47.356 1266 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.26), residues: 1044 helix: 1.30 (0.26), residues: 436 sheet: -0.89 (0.38), residues: 162 loop : -1.01 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 684 TYR 0.017 0.001 TYR D 711 PHE 0.009 0.001 PHE A 495 TRP 0.006 0.001 TRP B 671 HIS 0.001 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8538) covalent geometry : angle 0.47719 (11520) SS BOND : bond 0.00129 ( 4) SS BOND : angle 0.37929 ( 8) hydrogen bonds : bond 0.02758 ( 327) hydrogen bonds : angle 4.52279 ( 939) ********************** 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 152 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.226 Fit side-chains REVERT: A 647 TYR cc_start: 0.8063 (p90) cc_final: 0.7771 (p90) REVERT: A 714 GLN cc_start: 0.7407 (mp10) cc_final: 0.6988 (mp10) REVERT: B 756 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.6730 (mt0) REVERT: B 765 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8185 (tttt) REVERT: C 407 MET cc_start: 0.8310 (mpp) cc_final: 0.7605 (mtt) REVERT: C 408 MET cc_start: 0.7998 (tpp) cc_final: 0.7659 (tpp) outliers start: 23 outliers final: 19 residues processed: 148 average time/residue: 0.1196 time to fit residues: 22.5604 Evaluate side-chains 150 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 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 718 CYS 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 D residue 399 THR 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 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 8 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 0.0980 chunk 75 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 28 optimal weight: 0.0370 chunk 45 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.5660 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.154609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.130130 restraints weight = 10444.302| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.02 r_work: 0.3387 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1877 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= 0.095 Angle : 0.454 5.457 11528 Z= 0.230 Chirality : 0.042 0.166 1284 Planarity : 0.004 0.045 1422 Dihedral : 5.697 45.417 1266 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.26), residues: 1044 helix: 1.39 (0.26), residues: 436 sheet: -0.88 (0.38), residues: 162 loop : -0.98 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 684 TYR 0.017 0.001 TYR D 711 PHE 0.008 0.001 PHE D 495 TRP 0.006 0.001 TRP B 671 HIS 0.001 0.000 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 8538) covalent geometry : angle 0.45427 (11520) SS BOND : bond 0.00094 ( 4) SS BOND : angle 0.26584 ( 8) hydrogen bonds : bond 0.02488 ( 327) hydrogen bonds : angle 4.49198 ( 939) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2131.36 seconds wall clock time: 37 minutes 12.28 seconds (2232.28 seconds total)