Starting phenix.real_space_refine on Tue Mar 3 19:55:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fqa_29381/03_2026/8fqa_29381.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fqa_29381/03_2026/8fqa_29381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fqa_29381/03_2026/8fqa_29381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fqa_29381/03_2026/8fqa_29381.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fqa_29381/03_2026/8fqa_29381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fqa_29381/03_2026/8fqa_29381.map" } resolution = 3.35 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= 0.002 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 1602 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8386 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': 2, 'PTRANS': 8, '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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.05, per 1000 atoms: 0.24 Number of scatterers: 8386 At special positions: 0 Unit cell: (115.55, 87.6865, 84.4085, 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 1602 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: 0.63 Conformation dependent library (CDL) restraints added in 265.1 milliseconds 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 23 sheets defined 42.7% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.726A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 420 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 462 through 469 Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.745A 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 653 through 662 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 416 through 419 removed outlier: 3.718A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 436 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 removed outlier: 3.600A pdb=" N LEU B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 664 through 675 Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'C' and resid 416 through 419 removed outlier: 4.311A 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 462 through 469 Processing helix chain 'C' and resid 482 through 487 removed outlier: 3.866A pdb=" N GLU C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 642 Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 696 Processing helix chain 'C' and resid 705 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 416 through 419 removed outlier: 3.907A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 436 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 635 through 642 Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 664 through 677 removed outlier: 3.542A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 768 Processing sheet with id=AA1, first strand: chain 'A' and resid 395 through 399 removed outlier: 6.381A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.860A pdb=" N ALA A 452 " --> pdb=" O ASN A 461 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN A 461 " --> pdb=" O ALA A 452 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA4, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.988A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 649 removed outlier: 6.591A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 394 through 399 removed outlier: 6.983A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'B' and resid 490 through 491 Processing sheet with id=AA9, first strand: chain 'B' and resid 496 through 498 removed outlier: 4.035A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.592A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 723 " --> pdb=" O ILE B 502 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE B 504 " --> pdb=" O MET B 721 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 395 through 399 Processing sheet with id=AB3, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB4, first strand: chain 'C' and resid 451 through 453 removed outlier: 3.878A pdb=" N ALA C 452 " --> pdb=" O ASN C 461 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN C 461 " --> pdb=" O ALA C 452 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AB6, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.985A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 502 through 505 removed outlier: 4.243A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL C 723 " --> pdb=" O ILE C 502 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE C 504 " --> pdb=" O MET C 721 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 646 through 648 Processing sheet with id=AB9, first strand: chain 'D' and resid 439 through 444 removed outlier: 3.591A pdb=" N LYS D 441 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL D 397 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC2, first strand: chain 'D' and resid 453 through 454 removed outlier: 3.685A pdb=" N ILE D 459 " --> pdb=" O ASP D 454 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 490 through 491 Processing sheet with id=AC4, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.899A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.953A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 328 hydrogen bonds defined for protein. 945 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.22 Time building geometry restraints manager: 0.85 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: 2038 1.48 - 1.60: 3726 1.60 - 1.72: 40 1.72 - 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 1.577 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C3 CYZ A1302 " pdb=" C4 CYZ A1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C3 CYZ C1302 " pdb=" C4 CYZ C1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.47e+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 C1302 " pdb=" C6 CYZ C1302 " ideal model delta sigma weight residual 1.553 1.330 0.223 2.00e-02 2.50e+03 1.24e+02 ... (remaining 8533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 11259 1.88 - 3.76: 170 3.76 - 5.63: 45 5.63 - 7.51: 28 7.51 - 9.39: 18 Bond angle restraints: 11520 Sorted by residual: angle pdb=" C9 CYZ C1302 " pdb=" S1 CYZ C1302 " pdb=" N1 CYZ C1302 " ideal model delta sigma weight residual 101.75 111.14 -9.39 3.00e+00 1.11e-01 9.79e+00 angle pdb=" N GLY A 423 " pdb=" CA GLY A 423 " pdb=" C GLY A 423 " ideal model delta sigma weight residual 110.56 114.81 -4.25 1.36e+00 5.41e-01 9.77e+00 angle pdb=" N GLU B 678 " pdb=" CA GLU B 678 " pdb=" C GLU B 678 " ideal model delta sigma weight residual 109.81 116.67 -6.86 2.21e+00 2.05e-01 9.64e+00 angle pdb=" C9 CYZ B1302 " pdb=" S1 CYZ B1302 " pdb=" N1 CYZ B1302 " ideal model delta sigma weight residual 101.75 111.05 -9.30 3.00e+00 1.11e-01 9.60e+00 angle pdb=" C9 CYZ A1302 " pdb=" S1 CYZ A1302 " pdb=" N1 CYZ A1302 " ideal model delta sigma weight residual 101.75 111.01 -9.26 3.00e+00 1.11e-01 9.53e+00 ... (remaining 11515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.01: 4653 23.01 - 46.02: 477 46.02 - 69.04: 89 69.04 - 92.05: 17 92.05 - 115.06: 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 -164.19 78.19 1 1.00e+01 1.00e-02 7.63e+01 dihedral pdb=" CA GLU B 678 " pdb=" C GLU B 678 " pdb=" N PRO B 679 " pdb=" CA PRO B 679 " ideal model delta harmonic sigma weight residual 180.00 138.94 41.06 0 5.00e+00 4.00e-02 6.75e+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 93.00 163.84 -70.84 1 1.00e+01 1.00e-02 6.45e+01 ... (remaining 5245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1178 0.087 - 0.173: 90 0.173 - 0.260: 0 0.260 - 0.346: 0 0.346 - 0.433: 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 -0.43 2.00e-01 2.50e+01 4.68e+00 chirality pdb=" C2 CYZ D1302 " pdb=" C1 CYZ D1302 " pdb=" C3 CYZ D1302 " pdb=" C7 CYZ D1302 " both_signs ideal model delta sigma weight residual False 3.31 2.88 0.42 2.00e-01 2.50e+01 4.50e+00 chirality pdb=" C2 CYZ B1302 " pdb=" C1 CYZ B1302 " pdb=" C3 CYZ B1302 " pdb=" C7 CYZ B1302 " both_signs ideal model delta sigma weight residual False 3.31 2.89 0.42 2.00e-01 2.50e+01 4.50e+00 ... (remaining 1281 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 678 " -0.070 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO B 679 " 0.188 5.00e-02 4.00e+02 pdb=" CA PRO B 679 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO B 679 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 716 " 0.045 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO A 717 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 717 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 717 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 716 " -0.037 5.00e-02 4.00e+02 5.68e-02 5.17e+00 pdb=" N PRO C 717 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 717 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 717 " -0.029 5.00e-02 4.00e+02 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1299 2.76 - 3.29: 7943 3.29 - 3.83: 14042 3.83 - 4.36: 16281 4.36 - 4.90: 28460 Nonbonded interactions: 68025 Sorted by model distance: nonbonded pdb=" O ARG B 692 " pdb=" OG SER B 696 " model vdw 2.225 3.040 nonbonded pdb=" OD1 ASP D 728 " pdb=" N SER D 729 " model vdw 2.229 3.120 nonbonded pdb=" OE2 GLU D 705 " pdb=" O HOH D1401 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR A 424 " pdb=" O HOH A1401 " model vdw 2.237 3.040 nonbonded pdb=" OH TYR C 424 " pdb=" O HOH C1401 " model vdw 2.242 3.040 ... (remaining 68020 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: 4.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.020 Find NCS groups from input model: 0.190 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 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 0.243 8542 Z= 0.726 Angle : 0.744 9.388 11528 Z= 0.327 Chirality : 0.062 0.433 1284 Planarity : 0.005 0.109 1422 Dihedral : 19.079 115.061 3288 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.34 % Allowed : 30.43 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 30.56 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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 are not related in a simple way. whole: 0.12 (0.26), residues: 1044 helix: 1.42 (0.26), residues: 416 sheet: -0.34 (0.42), residues: 160 loop : -0.99 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 715 TYR 0.012 0.001 TYR B 732 PHE 0.007 0.001 PHE C 495 TRP 0.007 0.001 TRP A 671 HIS 0.001 0.001 HIS C 435 Details of bonding type rmsd covalent geometry : bond 0.01456 ( 8538) covalent geometry : angle 0.74368 (11520) SS BOND : bond 0.00172 ( 4) SS BOND : angle 0.47614 ( 8) hydrogen bonds : bond 0.17486 ( 328) hydrogen bonds : angle 6.67586 ( 945) *********************** 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 174 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 171 time to evaluate : 0.329 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 172 average time/residue: 0.1139 time to fit residues: 25.8558 Evaluate side-chains 167 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.1980 chunk 38 optimal weight: 0.0030 chunk 61 optimal weight: 3.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.169468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.147683 restraints weight = 13839.637| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.86 r_work: 0.3766 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8542 Z= 0.118 Angle : 0.537 7.078 11528 Z= 0.274 Chirality : 0.043 0.148 1284 Planarity : 0.004 0.081 1422 Dihedral : 10.608 100.469 1268 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.80 % Allowed : 27.18 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 30.56 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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 are not related in a simple way. whole: -0.02 (0.26), residues: 1044 helix: 1.28 (0.25), residues: 442 sheet: -0.58 (0.43), residues: 142 loop : -1.10 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 715 TYR 0.017 0.001 TYR D 702 PHE 0.009 0.001 PHE C 667 TRP 0.009 0.001 TRP A 671 HIS 0.002 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8538) covalent geometry : angle 0.53679 (11520) SS BOND : bond 0.00177 ( 4) SS BOND : angle 0.70978 ( 8) hydrogen bonds : bond 0.03270 ( 328) hydrogen bonds : angle 4.91828 ( 945) *********************** 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 202 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: B 411 ASN cc_start: 0.7368 (p0) cc_final: 0.7141 (p0) REVERT: B 476 ILE cc_start: 0.8897 (mp) cc_final: 0.8612 (mt) REVERT: C 697 LYS cc_start: 0.8325 (mttp) cc_final: 0.7242 (tptp) REVERT: C 705 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7237 (mt-10) REVERT: D 414 MET cc_start: 0.6202 (pmm) cc_final: 0.5439 (pmm) REVERT: D 442 LEU cc_start: 0.8479 (mt) cc_final: 0.8273 (mp) outliers start: 25 outliers final: 9 residues processed: 194 average time/residue: 0.1153 time to fit residues: 29.4267 Evaluate side-chains 174 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 164 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 755 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 100 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 ASN A 756 GLN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.168977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.147070 restraints weight = 13832.040| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.86 r_work: 0.3760 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1382 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= 0.111 Angle : 0.525 7.244 11528 Z= 0.267 Chirality : 0.043 0.149 1284 Planarity : 0.004 0.054 1422 Dihedral : 10.146 99.030 1266 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.24 % Allowed : 26.06 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 30.56 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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 are not related in a simple way. whole: -0.02 (0.26), residues: 1044 helix: 1.23 (0.25), residues: 442 sheet: -0.41 (0.41), residues: 156 loop : -1.12 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 684 TYR 0.016 0.001 TYR D 702 PHE 0.007 0.001 PHE C 667 TRP 0.007 0.001 TRP B 460 HIS 0.003 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8538) covalent geometry : angle 0.52520 (11520) SS BOND : bond 0.00144 ( 4) SS BOND : angle 0.64754 ( 8) hydrogen bonds : bond 0.03040 ( 328) hydrogen bonds : angle 4.65609 ( 945) *********************** 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 211 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 660 ARG cc_start: 0.8046 (tpp80) cc_final: 0.7826 (tpp80) REVERT: A 705 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7208 (mm-30) REVERT: B 411 ASN cc_start: 0.7311 (p0) cc_final: 0.6953 (p0) REVERT: B 476 ILE cc_start: 0.8862 (mp) cc_final: 0.8590 (mt) REVERT: B 688 GLU cc_start: 0.8401 (tp30) cc_final: 0.8130 (tp30) REVERT: C 697 LYS cc_start: 0.8369 (mttp) cc_final: 0.7256 (tptp) REVERT: C 705 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7237 (mt-10) REVERT: D 414 MET cc_start: 0.6224 (pmm) cc_final: 0.5743 (pmm) REVERT: D 453 ARG cc_start: 0.7350 (ttt90) cc_final: 0.6928 (ttm-80) REVERT: D 719 ASP cc_start: 0.7264 (p0) cc_final: 0.6973 (p0) outliers start: 29 outliers final: 17 residues processed: 198 average time/residue: 0.1102 time to fit residues: 28.8224 Evaluate side-chains 182 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 769 ASP Chi-restraints excluded: chain D residue 723 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 43 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 49 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.167461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.145776 restraints weight = 14104.599| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.79 r_work: 0.3744 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1645 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= 0.129 Angle : 0.539 6.730 11528 Z= 0.275 Chirality : 0.044 0.211 1284 Planarity : 0.004 0.038 1422 Dihedral : 9.976 101.261 1266 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.47 % Allowed : 26.85 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 30.56 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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 are not related in a simple way. whole: -0.06 (0.26), residues: 1044 helix: 1.22 (0.25), residues: 438 sheet: -0.43 (0.41), residues: 152 loop : -1.12 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 628 TYR 0.016 0.001 TYR C 673 PHE 0.010 0.001 PHE C 667 TRP 0.005 0.001 TRP D 460 HIS 0.003 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8538) covalent geometry : angle 0.53894 (11520) SS BOND : bond 0.00209 ( 4) SS BOND : angle 0.73563 ( 8) hydrogen bonds : bond 0.03102 ( 328) hydrogen bonds : angle 4.59649 ( 945) *********************** 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 207 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 674 MET cc_start: 0.7998 (mtm) cc_final: 0.7741 (mtp) REVERT: B 411 ASN cc_start: 0.7279 (p0) cc_final: 0.6908 (p0) REVERT: B 476 ILE cc_start: 0.8851 (mp) cc_final: 0.8581 (mt) REVERT: B 688 GLU cc_start: 0.8418 (tp30) cc_final: 0.8114 (tp30) REVERT: C 704 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7758 (pt) REVERT: C 705 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7280 (mt-10) REVERT: D 414 MET cc_start: 0.6237 (pmm) cc_final: 0.5868 (pmm) REVERT: D 453 ARG cc_start: 0.7518 (ttt90) cc_final: 0.7134 (ttm-80) REVERT: D 634 GLU cc_start: 0.7178 (tp30) cc_final: 0.6919 (tp30) REVERT: D 719 ASP cc_start: 0.7426 (p0) cc_final: 0.7091 (p0) REVERT: D 722 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8375 (tttp) REVERT: D 755 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6932 (tp30) outliers start: 31 outliers final: 21 residues processed: 197 average time/residue: 0.1050 time to fit residues: 27.3335 Evaluate side-chains 184 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 722 LYS Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 755 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 37 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 81 optimal weight: 0.4980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 ASN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.167347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.145605 restraints weight = 14029.363| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.79 r_work: 0.3739 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8542 Z= 0.130 Angle : 0.537 6.396 11528 Z= 0.276 Chirality : 0.044 0.158 1284 Planarity : 0.004 0.034 1422 Dihedral : 9.898 100.892 1266 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.81 % Allowed : 25.73 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 30.56 % 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 are not related in a simple way. whole: -0.17 (0.26), residues: 1044 helix: 1.18 (0.25), residues: 438 sheet: -0.66 (0.40), residues: 156 loop : -1.19 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 628 TYR 0.013 0.001 TYR D 702 PHE 0.010 0.001 PHE C 667 TRP 0.006 0.001 TRP A 671 HIS 0.003 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8538) covalent geometry : angle 0.53657 (11520) SS BOND : bond 0.00255 ( 4) SS BOND : angle 0.76929 ( 8) hydrogen bonds : bond 0.03122 ( 328) hydrogen bonds : angle 4.58101 ( 945) *********************** 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 207 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 164 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 674 MET cc_start: 0.8021 (mtm) cc_final: 0.7773 (mtp) REVERT: B 411 ASN cc_start: 0.7159 (p0) cc_final: 0.6758 (p0) REVERT: B 476 ILE cc_start: 0.8852 (mp) cc_final: 0.8593 (mt) REVERT: C 456 ASP cc_start: 0.4680 (OUTLIER) cc_final: 0.3673 (t0) REVERT: C 498 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8153 (pp) REVERT: C 697 LYS cc_start: 0.8336 (mttp) cc_final: 0.7257 (tptp) REVERT: C 704 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7743 (pt) REVERT: C 705 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7315 (mt-10) REVERT: D 414 MET cc_start: 0.6202 (pmm) cc_final: 0.5962 (pmm) REVERT: D 453 ARG cc_start: 0.7465 (ttt90) cc_final: 0.7056 (ttm-80) REVERT: D 634 GLU cc_start: 0.7163 (tp30) cc_final: 0.6813 (tp30) REVERT: D 684 ARG cc_start: 0.7287 (tpp80) cc_final: 0.7005 (tpt-90) REVERT: D 728 ASP cc_start: 0.7706 (t0) cc_final: 0.7451 (t0) REVERT: D 755 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6915 (tp30) outliers start: 43 outliers final: 28 residues processed: 195 average time/residue: 0.1027 time to fit residues: 26.3355 Evaluate side-chains 188 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 769 ASP Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 755 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 15 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 ASN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.165268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.143714 restraints weight = 14025.440| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.71 r_work: 0.3723 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2138 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= 0.176 Angle : 0.582 6.841 11528 Z= 0.300 Chirality : 0.045 0.160 1284 Planarity : 0.004 0.034 1422 Dihedral : 10.460 105.768 1266 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.47 % Allowed : 26.51 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 30.56 % 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 are not related in a simple way. whole: -0.35 (0.26), residues: 1044 helix: 1.02 (0.25), residues: 434 sheet: -0.83 (0.39), residues: 166 loop : -1.23 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 684 TYR 0.015 0.002 TYR B 673 PHE 0.015 0.002 PHE C 667 TRP 0.005 0.001 TRP D 460 HIS 0.004 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 8538) covalent geometry : angle 0.58166 (11520) SS BOND : bond 0.00339 ( 4) SS BOND : angle 0.87834 ( 8) hydrogen bonds : bond 0.03609 ( 328) hydrogen bonds : angle 4.71864 ( 945) *********************** 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 198 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: B 411 ASN cc_start: 0.7049 (p0) cc_final: 0.6665 (p0) REVERT: B 466 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6478 (tt0) REVERT: C 456 ASP cc_start: 0.4579 (OUTLIER) cc_final: 0.3561 (t0) REVERT: C 498 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8442 (pp) REVERT: C 704 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7782 (pt) REVERT: C 705 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7494 (mt-10) REVERT: D 414 MET cc_start: 0.6232 (pmm) cc_final: 0.5982 (pmm) REVERT: D 442 LEU cc_start: 0.8428 (mt) cc_final: 0.8152 (mp) REVERT: D 453 ARG cc_start: 0.7459 (ttt90) cc_final: 0.7113 (ttm-80) REVERT: D 684 ARG cc_start: 0.7285 (tpp80) cc_final: 0.7020 (tpt-90) outliers start: 40 outliers final: 31 residues processed: 184 average time/residue: 0.1075 time to fit residues: 26.0764 Evaluate side-chains 189 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 153 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 769 ASP Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 755 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 97 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 22 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.168004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.146524 restraints weight = 14204.581| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.78 r_work: 0.3749 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8542 Z= 0.114 Angle : 0.542 6.359 11528 Z= 0.278 Chirality : 0.043 0.166 1284 Planarity : 0.003 0.031 1422 Dihedral : 9.750 98.132 1266 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.03 % Allowed : 27.18 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 30.56 % 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 are not related in a simple way. whole: -0.29 (0.26), residues: 1044 helix: 1.08 (0.25), residues: 438 sheet: -0.61 (0.41), residues: 152 loop : -1.30 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 684 TYR 0.014 0.001 TYR B 673 PHE 0.006 0.001 PHE C 667 TRP 0.011 0.001 TRP B 460 HIS 0.002 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8538) covalent geometry : angle 0.54162 (11520) SS BOND : bond 0.00167 ( 4) SS BOND : angle 0.60840 ( 8) hydrogen bonds : bond 0.02987 ( 328) hydrogen bonds : angle 4.58001 ( 945) *********************** 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 208 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 411 ASN cc_start: 0.7036 (p0) cc_final: 0.6663 (p0) REVERT: B 476 ILE cc_start: 0.8870 (mp) cc_final: 0.8552 (mt) REVERT: B 661 ARG cc_start: 0.7426 (tpm170) cc_final: 0.6721 (ttm-80) REVERT: C 498 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8426 (pp) REVERT: C 697 LYS cc_start: 0.8350 (mttp) cc_final: 0.7270 (tptp) REVERT: C 705 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7422 (mt-10) REVERT: D 453 ARG cc_start: 0.7381 (ttt90) cc_final: 0.7049 (ttm-80) REVERT: D 684 ARG cc_start: 0.7283 (tpp80) cc_final: 0.7046 (tpt-90) REVERT: D 713 GLU cc_start: 0.7121 (tt0) cc_final: 0.6831 (tt0) REVERT: D 715 ARG cc_start: 0.7410 (ttm-80) cc_final: 0.7153 (ttm-80) REVERT: D 719 ASP cc_start: 0.7580 (p0) cc_final: 0.7146 (p0) REVERT: D 755 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.6978 (tp30) outliers start: 36 outliers final: 24 residues processed: 194 average time/residue: 0.1078 time to fit residues: 27.8668 Evaluate side-chains 185 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 755 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 104 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 ASN A 756 GLN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 756 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.168482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.146735 restraints weight = 13726.067| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.83 r_work: 0.3752 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8542 Z= 0.108 Angle : 0.543 6.756 11528 Z= 0.277 Chirality : 0.043 0.169 1284 Planarity : 0.003 0.030 1422 Dihedral : 9.502 96.652 1266 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.58 % Allowed : 28.08 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 30.56 % 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 are not related in a simple way. whole: -0.29 (0.26), residues: 1044 helix: 1.09 (0.25), residues: 440 sheet: -0.64 (0.41), residues: 156 loop : -1.32 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 684 TYR 0.013 0.001 TYR B 673 PHE 0.006 0.001 PHE C 495 TRP 0.010 0.001 TRP B 460 HIS 0.002 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 8538) covalent geometry : angle 0.54323 (11520) SS BOND : bond 0.00128 ( 4) SS BOND : angle 0.46136 ( 8) hydrogen bonds : bond 0.02976 ( 328) hydrogen bonds : angle 4.52710 ( 945) *********************** 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 206 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 674 MET cc_start: 0.7917 (mtm) cc_final: 0.7649 (mtp) REVERT: A 705 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7217 (mm-30) REVERT: B 411 ASN cc_start: 0.7117 (p0) cc_final: 0.6732 (p0) REVERT: B 456 ASP cc_start: 0.4028 (OUTLIER) cc_final: 0.3179 (t70) REVERT: B 476 ILE cc_start: 0.8885 (mp) cc_final: 0.8584 (mt) REVERT: B 661 ARG cc_start: 0.7448 (tpm170) cc_final: 0.6943 (mtp85) REVERT: B 688 GLU cc_start: 0.8342 (tp30) cc_final: 0.8024 (tp30) REVERT: C 486 GLU cc_start: 0.6364 (mm-30) cc_final: 0.6151 (mt-10) REVERT: C 498 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8404 (pp) REVERT: C 697 LYS cc_start: 0.8405 (mttp) cc_final: 0.7244 (tptp) REVERT: C 705 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7393 (mt-10) REVERT: D 453 ARG cc_start: 0.7339 (ttt90) cc_final: 0.7031 (ttm-80) REVERT: D 684 ARG cc_start: 0.7345 (tpp80) cc_final: 0.7094 (tpt-90) REVERT: D 715 ARG cc_start: 0.7471 (ttm-80) cc_final: 0.7118 (mpt180) REVERT: D 719 ASP cc_start: 0.7448 (p0) cc_final: 0.7081 (p0) REVERT: D 755 GLU cc_start: 0.7483 (tp30) cc_final: 0.7231 (tp30) outliers start: 32 outliers final: 24 residues processed: 197 average time/residue: 0.1080 time to fit residues: 28.2901 Evaluate side-chains 195 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 736 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 59 optimal weight: 0.0060 chunk 54 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 overall best weight: 1.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 ASN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.167501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.145847 restraints weight = 13817.188| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.79 r_work: 0.3741 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8542 Z= 0.123 Angle : 0.557 6.991 11528 Z= 0.284 Chirality : 0.043 0.173 1284 Planarity : 0.003 0.030 1422 Dihedral : 9.711 100.599 1266 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.69 % Allowed : 28.64 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 30.56 % 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 are not related in a simple way. whole: -0.30 (0.26), residues: 1044 helix: 1.05 (0.25), residues: 440 sheet: -0.58 (0.42), residues: 152 loop : -1.31 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 684 TYR 0.017 0.001 TYR B 673 PHE 0.008 0.001 PHE C 667 TRP 0.014 0.001 TRP D 766 HIS 0.002 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8538) covalent geometry : angle 0.55717 (11520) SS BOND : bond 0.00168 ( 4) SS BOND : angle 0.58317 ( 8) hydrogen bonds : bond 0.03106 ( 328) hydrogen bonds : angle 4.54871 ( 945) *********************** 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 196 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 674 MET cc_start: 0.7837 (mtm) cc_final: 0.7603 (mtp) REVERT: A 705 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7244 (mm-30) REVERT: B 411 ASN cc_start: 0.7133 (p0) cc_final: 0.6748 (p0) REVERT: B 456 ASP cc_start: 0.3975 (OUTLIER) cc_final: 0.2990 (t0) REVERT: B 476 ILE cc_start: 0.8882 (mp) cc_final: 0.8581 (mt) REVERT: B 661 ARG cc_start: 0.7443 (tpm170) cc_final: 0.6994 (mtp85) REVERT: B 673 TYR cc_start: 0.5235 (m-10) cc_final: 0.4950 (t80) REVERT: B 688 GLU cc_start: 0.8397 (tp30) cc_final: 0.8058 (tp30) REVERT: C 498 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8393 (pp) REVERT: C 697 LYS cc_start: 0.8398 (mttp) cc_final: 0.7296 (tptp) REVERT: C 704 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7744 (pt) REVERT: C 705 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7429 (mt-10) REVERT: D 684 ARG cc_start: 0.7320 (tpp80) cc_final: 0.7082 (tpt-90) REVERT: D 719 ASP cc_start: 0.7469 (p0) cc_final: 0.7102 (p0) REVERT: D 752 LYS cc_start: 0.8464 (tptt) cc_final: 0.8193 (tppt) outliers start: 33 outliers final: 28 residues processed: 188 average time/residue: 0.1018 time to fit residues: 25.6460 Evaluate side-chains 193 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 736 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 76 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 84 optimal weight: 0.0270 chunk 79 optimal weight: 0.7980 overall best weight: 1.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 ASN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.167096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.145401 restraints weight = 13764.888| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.80 r_work: 0.3739 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8542 Z= 0.128 Angle : 0.562 7.994 11528 Z= 0.286 Chirality : 0.044 0.172 1284 Planarity : 0.003 0.029 1422 Dihedral : 9.830 101.378 1266 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.80 % Allowed : 28.64 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 30.56 % 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 are not related in a simple way. whole: -0.29 (0.26), residues: 1044 helix: 1.06 (0.25), residues: 438 sheet: -0.92 (0.47), residues: 126 loop : -1.15 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 684 TYR 0.015 0.001 TYR B 673 PHE 0.009 0.001 PHE C 667 TRP 0.012 0.001 TRP B 460 HIS 0.002 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8538) covalent geometry : angle 0.56211 (11520) SS BOND : bond 0.00189 ( 4) SS BOND : angle 0.62820 ( 8) hydrogen bonds : bond 0.03109 ( 328) hydrogen bonds : angle 4.56750 ( 945) ********************** 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 195 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 705 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7266 (mm-30) REVERT: B 411 ASN cc_start: 0.7082 (p0) cc_final: 0.6704 (p0) REVERT: B 456 ASP cc_start: 0.4014 (OUTLIER) cc_final: 0.3107 (t70) REVERT: B 476 ILE cc_start: 0.8876 (mp) cc_final: 0.8575 (mt) REVERT: B 661 ARG cc_start: 0.7421 (tpm170) cc_final: 0.6970 (mtp85) REVERT: B 673 TYR cc_start: 0.5356 (m-10) cc_final: 0.5006 (t80) REVERT: B 688 GLU cc_start: 0.8393 (tp30) cc_final: 0.8066 (tp30) REVERT: C 498 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8393 (pp) REVERT: C 697 LYS cc_start: 0.8409 (mttp) cc_final: 0.7294 (tptp) REVERT: C 704 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7781 (pt) REVERT: C 705 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7438 (mt-10) REVERT: D 684 ARG cc_start: 0.7333 (tpp80) cc_final: 0.7092 (tpt-90) REVERT: D 713 GLU cc_start: 0.7376 (tt0) cc_final: 0.7109 (tt0) REVERT: D 715 ARG cc_start: 0.7409 (ttm-80) cc_final: 0.7125 (mpt180) REVERT: D 719 ASP cc_start: 0.7512 (p0) cc_final: 0.7152 (p0) REVERT: D 752 LYS cc_start: 0.8449 (tptt) cc_final: 0.8185 (tppt) outliers start: 34 outliers final: 29 residues processed: 186 average time/residue: 0.0980 time to fit residues: 24.2049 Evaluate side-chains 192 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 769 ASP Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 736 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 14 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 100 optimal weight: 0.4980 chunk 88 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 102 optimal weight: 0.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 ASN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.164780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.143006 restraints weight = 14069.638| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.74 r_work: 0.3712 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8542 Z= 0.189 Angle : 0.613 8.741 11528 Z= 0.315 Chirality : 0.046 0.185 1284 Planarity : 0.004 0.035 1422 Dihedral : 10.614 107.525 1266 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.47 % Allowed : 28.41 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 30.56 % 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 are not related in a simple way. whole: -0.39 (0.25), residues: 1044 helix: 1.00 (0.25), residues: 420 sheet: -0.77 (0.45), residues: 140 loop : -1.22 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 628 TYR 0.016 0.002 TYR A 424 PHE 0.015 0.002 PHE C 667 TRP 0.014 0.001 TRP B 460 HIS 0.003 0.001 HIS C 435 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 8538) covalent geometry : angle 0.61273 (11520) SS BOND : bond 0.00342 ( 4) SS BOND : angle 1.04998 ( 8) hydrogen bonds : bond 0.03705 ( 328) hydrogen bonds : angle 4.73742 ( 945) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1762.37 seconds wall clock time: 31 minutes 1.43 seconds (1861.43 seconds total)