Starting phenix.real_space_refine on Sun May 11 21:11:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fqa_29381/05_2025/8fqa_29381.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fqa_29381/05_2025/8fqa_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8fqa_29381/05_2025/8fqa_29381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fqa_29381/05_2025/8fqa_29381.map" model { file = "/net/cci-nas-00/data/ceres_data/8fqa_29381/05_2025/8fqa_29381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fqa_29381/05_2025/8fqa_29381.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.89, per 1000 atoms: 0.70 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: 2.11 Conformation dependent library (CDL) restraints added in 1.0 seconds 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 23 sheets defined 42.7% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 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: 2.22 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2630 1.35 - 1.48: 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'B' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 773 or resid 1301 or resid 1302)) selection = (chain 'C' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'D' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 773 or resid 1301 or resid 1302)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.270 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.180 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.150 ------------------------------------------------------------------------------- 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 : 9.52 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (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 TRP 0.007 0.001 TRP A 671 HIS 0.001 0.001 HIS C 435 PHE 0.007 0.001 PHE C 495 TYR 0.012 0.001 TYR B 732 ARG 0.006 0.000 ARG D 715 Details of bonding type rmsd hydrogen bonds : bond 0.17486 ( 328) hydrogen bonds : angle 6.67586 ( 945) SS BOND : bond 0.00172 ( 4) SS BOND : angle 0.47614 ( 8) covalent geometry : bond 0.01456 ( 8538) covalent geometry : angle 0.74368 (11520) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 171 time to evaluate : 1.213 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 172 average time/residue: 0.2442 time to fit residues: 55.4005 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 : 0.948 ------------------------------------------------------------------------------- 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 89 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 0.0060 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 0.0570 chunk 42 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 overall best weight: 0.9516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.169523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.147761 restraints weight = 13756.352| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.86 r_work: 0.3767 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.0986 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= 0.119 Angle : 0.536 7.040 11528 Z= 0.274 Chirality : 0.043 0.147 1284 Planarity : 0.004 0.080 1422 Dihedral : 10.632 100.398 1268 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.68 % Allowed : 27.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.26), residues: 1044 helix: 1.28 (0.25), residues: 442 sheet: -0.57 (0.43), residues: 142 loop : -1.09 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 671 HIS 0.002 0.001 HIS C 412 PHE 0.008 0.001 PHE C 667 TYR 0.017 0.001 TYR D 702 ARG 0.004 0.000 ARG D 715 Details of bonding type rmsd hydrogen bonds : bond 0.03231 ( 328) hydrogen bonds : angle 4.91532 ( 945) SS BOND : bond 0.00174 ( 4) SS BOND : angle 0.73370 ( 8) covalent geometry : bond 0.00276 ( 8538) covalent geometry : angle 0.53607 (11520) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: B 411 ASN cc_start: 0.7371 (p0) cc_final: 0.7145 (p0) REVERT: B 476 ILE cc_start: 0.8894 (mp) cc_final: 0.8609 (mt) REVERT: C 697 LYS cc_start: 0.8334 (mttp) cc_final: 0.7245 (tptp) REVERT: C 705 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7270 (mt-10) REVERT: D 414 MET cc_start: 0.6204 (pmm) cc_final: 0.5442 (pmm) REVERT: D 442 LEU cc_start: 0.8476 (mt) cc_final: 0.8268 (mp) outliers start: 24 outliers final: 9 residues processed: 192 average time/residue: 0.2321 time to fit residues: 58.7630 Evaluate side-chains 175 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 165 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 83 optimal weight: 5.9990 chunk 69 optimal weight: 0.2980 chunk 85 optimal weight: 0.0060 chunk 52 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- 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** C 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 = 0.168676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.146627 restraints weight = 13983.253| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.89 r_work: 0.3754 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1398 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= 0.116 Angle : 0.527 7.203 11528 Z= 0.269 Chirality : 0.043 0.151 1284 Planarity : 0.004 0.053 1422 Dihedral : 10.279 100.002 1266 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.80 % Allowed : 25.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.26), residues: 1044 helix: 1.24 (0.25), residues: 440 sheet: -0.42 (0.41), residues: 156 loop : -1.15 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 460 HIS 0.003 0.001 HIS C 412 PHE 0.009 0.001 PHE C 667 TYR 0.017 0.001 TYR D 702 ARG 0.003 0.000 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.03088 ( 328) hydrogen bonds : angle 4.65864 ( 945) SS BOND : bond 0.00151 ( 4) SS BOND : angle 0.70044 ( 8) covalent geometry : bond 0.00271 ( 8538) covalent geometry : angle 0.52729 (11520) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 674 MET cc_start: 0.8030 (mtm) cc_final: 0.7735 (mtp) REVERT: B 411 ASN cc_start: 0.7282 (p0) cc_final: 0.6912 (p0) REVERT: B 476 ILE cc_start: 0.8870 (mp) cc_final: 0.8599 (mt) REVERT: B 688 GLU cc_start: 0.8418 (tp30) cc_final: 0.7966 (tp30) REVERT: C 697 LYS cc_start: 0.8379 (mttp) cc_final: 0.7256 (tptp) REVERT: C 705 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7252 (mt-10) REVERT: D 414 MET cc_start: 0.6234 (pmm) cc_final: 0.5740 (pmm) REVERT: D 453 ARG cc_start: 0.7401 (ttt90) cc_final: 0.6984 (ttm-80) REVERT: D 719 ASP cc_start: 0.7287 (p0) cc_final: 0.6992 (p0) outliers start: 34 outliers final: 19 residues processed: 198 average time/residue: 0.2228 time to fit residues: 58.5663 Evaluate side-chains 180 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 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 758 VAL 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 723 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 75 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.4089 r_free = 0.4089 target = 0.165566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.143643 restraints weight = 14039.470| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.80 r_work: 0.3718 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8542 Z= 0.175 Angle : 0.587 6.884 11528 Z= 0.302 Chirality : 0.046 0.191 1284 Planarity : 0.004 0.041 1422 Dihedral : 10.804 106.270 1266 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.91 % Allowed : 26.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.25), residues: 1044 helix: 1.00 (0.25), residues: 438 sheet: -0.71 (0.40), residues: 152 loop : -1.26 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 460 HIS 0.003 0.001 HIS A 435 PHE 0.017 0.002 PHE C 667 TYR 0.018 0.002 TYR D 702 ARG 0.003 0.000 ARG B 628 Details of bonding type rmsd hydrogen bonds : bond 0.03590 ( 328) hydrogen bonds : angle 4.74777 ( 945) SS BOND : bond 0.00371 ( 4) SS BOND : angle 0.99744 ( 8) covalent geometry : bond 0.00413 ( 8538) covalent geometry : angle 0.58700 (11520) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: B 411 ASN cc_start: 0.7230 (p0) cc_final: 0.6825 (p0) REVERT: C 498 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8432 (pp) REVERT: C 704 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7776 (pt) REVERT: C 705 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7472 (mt-10) REVERT: D 414 MET cc_start: 0.6213 (pmm) cc_final: 0.5756 (pmm) REVERT: D 442 LEU cc_start: 0.8446 (mt) cc_final: 0.8240 (mp) REVERT: D 453 ARG cc_start: 0.7546 (ttt90) cc_final: 0.7140 (ttm-80) REVERT: D 496 MET cc_start: 0.8720 (ttt) cc_final: 0.8446 (ttt) REVERT: D 634 GLU cc_start: 0.7332 (tp30) cc_final: 0.6953 (tp30) REVERT: D 719 ASP cc_start: 0.7614 (p0) cc_final: 0.7209 (p0) outliers start: 35 outliers final: 25 residues processed: 194 average time/residue: 0.2313 time to fit residues: 59.3769 Evaluate side-chains 177 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 473 ASP Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 751 LEU 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 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 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 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 0 optimal weight: 8.9990 chunk 47 optimal weight: 0.0570 chunk 65 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 overall best weight: 1.0900 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.167081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.145181 restraints weight = 13799.081| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.82 r_work: 0.3733 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1954 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= 0.121 Angle : 0.528 6.455 11528 Z= 0.272 Chirality : 0.043 0.159 1284 Planarity : 0.003 0.031 1422 Dihedral : 9.924 99.349 1266 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.58 % Allowed : 27.29 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 30.56 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.26), residues: 1044 helix: 1.13 (0.25), residues: 438 sheet: -0.70 (0.40), residues: 156 loop : -1.27 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 766 HIS 0.003 0.001 HIS C 412 PHE 0.007 0.001 PHE C 667 TYR 0.012 0.001 TYR D 702 ARG 0.001 0.000 ARG D 628 Details of bonding type rmsd hydrogen bonds : bond 0.03053 ( 328) hydrogen bonds : angle 4.61097 ( 945) SS BOND : bond 0.00176 ( 4) SS BOND : angle 0.69933 ( 8) covalent geometry : bond 0.00281 ( 8538) covalent geometry : angle 0.52828 (11520) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: A 674 MET cc_start: 0.8060 (mtm) cc_final: 0.7772 (mtp) REVERT: A 705 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7283 (mm-30) REVERT: B 411 ASN cc_start: 0.7278 (p0) cc_final: 0.6870 (p0) REVERT: B 476 ILE cc_start: 0.8884 (mp) cc_final: 0.8572 (mt) REVERT: C 456 ASP cc_start: 0.4742 (OUTLIER) cc_final: 0.3755 (t0) REVERT: C 697 LYS cc_start: 0.8377 (mttp) cc_final: 0.7241 (tptp) REVERT: C 705 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7280 (mt-10) REVERT: D 414 MET cc_start: 0.6282 (pmm) cc_final: 0.6004 (pmm) REVERT: D 442 LEU cc_start: 0.8472 (mt) cc_final: 0.8188 (mp) REVERT: D 453 ARG cc_start: 0.7458 (ttt90) cc_final: 0.6991 (ttm-80) REVERT: D 634 GLU cc_start: 0.7309 (tp30) cc_final: 0.7025 (tp30) REVERT: D 684 ARG cc_start: 0.7293 (tpp80) cc_final: 0.7022 (tpt-90) REVERT: D 715 ARG cc_start: 0.7479 (ttm-80) cc_final: 0.7138 (mpt180) REVERT: D 728 ASP cc_start: 0.7735 (t0) cc_final: 0.7458 (t0) REVERT: D 755 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6996 (tp30) outliers start: 32 outliers final: 20 residues processed: 186 average time/residue: 0.2295 time to fit residues: 56.4014 Evaluate side-chains 182 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 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 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 504 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 723 VAL 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 68 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 91 optimal weight: 0.0170 chunk 30 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 overall best weight: 0.7622 ------------------------------------------------------------------------------- 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** D 756 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.168389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.146733 restraints weight = 13947.481| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.78 r_work: 0.3754 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8542 Z= 0.106 Angle : 0.518 6.296 11528 Z= 0.266 Chirality : 0.043 0.159 1284 Planarity : 0.003 0.029 1422 Dihedral : 9.589 97.295 1266 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.69 % Allowed : 26.73 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 30.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.26), residues: 1044 helix: 1.18 (0.25), residues: 438 sheet: -0.70 (0.40), residues: 156 loop : -1.25 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 766 HIS 0.003 0.001 HIS C 412 PHE 0.006 0.001 PHE C 495 TYR 0.011 0.001 TYR A 673 ARG 0.001 0.000 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.02901 ( 328) hydrogen bonds : angle 4.53282 ( 945) SS BOND : bond 0.00136 ( 4) SS BOND : angle 0.50441 ( 8) covalent geometry : bond 0.00242 ( 8538) covalent geometry : angle 0.51798 (11520) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: A 674 MET cc_start: 0.8058 (mtm) cc_final: 0.7803 (mtp) REVERT: A 705 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7227 (mm-30) REVERT: B 411 ASN cc_start: 0.7103 (p0) cc_final: 0.6714 (p0) REVERT: B 466 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6305 (tt0) REVERT: B 476 ILE cc_start: 0.8852 (mp) cc_final: 0.8538 (mt) REVERT: B 661 ARG cc_start: 0.7409 (tpm170) cc_final: 0.6973 (mtp85) REVERT: B 688 GLU cc_start: 0.8337 (tp30) cc_final: 0.8044 (tp30) REVERT: C 456 ASP cc_start: 0.4623 (OUTLIER) cc_final: 0.3640 (t0) REVERT: C 498 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8377 (pp) REVERT: C 697 LYS cc_start: 0.8346 (mttp) cc_final: 0.7299 (tptp) REVERT: C 704 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7721 (pt) REVERT: C 705 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7359 (mt-10) REVERT: D 453 ARG cc_start: 0.7439 (ttt90) cc_final: 0.7036 (ttm-80) REVERT: D 684 ARG cc_start: 0.7294 (tpp80) cc_final: 0.7041 (tpt-90) REVERT: D 715 ARG cc_start: 0.7402 (ttm-80) cc_final: 0.7139 (mpt180) REVERT: D 728 ASP cc_start: 0.7724 (t0) cc_final: 0.7516 (t0) REVERT: D 755 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6869 (tp30) outliers start: 33 outliers final: 19 residues processed: 197 average time/residue: 0.2335 time to fit residues: 60.5763 Evaluate side-chains 187 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 751 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 466 GLU 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 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 443 THR 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 755 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 chunk 38 optimal weight: 0.1980 chunk 6 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 91 optimal weight: 0.0070 chunk 57 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 = 0.4134 r_free = 0.4134 target = 0.170133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.148431 restraints weight = 13897.337| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.86 r_work: 0.3772 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8542 Z= 0.098 Angle : 0.525 6.625 11528 Z= 0.264 Chirality : 0.042 0.161 1284 Planarity : 0.003 0.030 1422 Dihedral : 9.018 92.896 1266 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.91 % Allowed : 27.52 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 30.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.26), residues: 1044 helix: 1.22 (0.25), residues: 440 sheet: -0.48 (0.41), residues: 152 loop : -1.21 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 766 HIS 0.002 0.001 HIS C 412 PHE 0.006 0.001 PHE B 495 TYR 0.014 0.001 TYR B 673 ARG 0.002 0.000 ARG B 684 Details of bonding type rmsd hydrogen bonds : bond 0.02740 ( 328) hydrogen bonds : angle 4.47537 ( 945) SS BOND : bond 0.00092 ( 4) SS BOND : angle 0.54727 ( 8) covalent geometry : bond 0.00220 ( 8538) covalent geometry : angle 0.52508 (11520) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: A 674 MET cc_start: 0.8011 (mtm) cc_final: 0.7810 (mtp) REVERT: A 697 LYS cc_start: 0.8486 (mttp) cc_final: 0.7276 (tptp) REVERT: A 705 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7232 (mm-30) REVERT: B 411 ASN cc_start: 0.7146 (p0) cc_final: 0.6739 (p0) REVERT: B 476 ILE cc_start: 0.8847 (mp) cc_final: 0.8565 (mt) REVERT: B 661 ARG cc_start: 0.7239 (tpm170) cc_final: 0.6812 (mtp85) REVERT: B 688 GLU cc_start: 0.8361 (tp30) cc_final: 0.8066 (tp30) REVERT: C 498 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8383 (pp) REVERT: C 697 LYS cc_start: 0.8330 (mttp) cc_final: 0.7268 (tptp) REVERT: C 704 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7762 (pt) REVERT: C 705 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7423 (mt-10) REVERT: D 453 ARG cc_start: 0.7389 (ttt90) cc_final: 0.7046 (ttm-80) REVERT: D 684 ARG cc_start: 0.7329 (tpp80) cc_final: 0.7079 (tpt-90) REVERT: D 719 ASP cc_start: 0.7326 (p0) cc_final: 0.6955 (p0) REVERT: D 728 ASP cc_start: 0.7665 (t0) cc_final: 0.7455 (t0) REVERT: D 755 GLU cc_start: 0.7385 (tp30) cc_final: 0.7180 (tp30) outliers start: 26 outliers final: 19 residues processed: 192 average time/residue: 0.2258 time to fit residues: 57.1044 Evaluate side-chains 178 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 751 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 410 LYS 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 91 optimal weight: 0.0870 chunk 75 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 overall best weight: 1.7362 ------------------------------------------------------------------------------- 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 = 0.4097 r_free = 0.4097 target = 0.166344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.144674 restraints weight = 14101.603| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.72 r_work: 0.3733 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8542 Z= 0.164 Angle : 0.588 6.884 11528 Z= 0.301 Chirality : 0.045 0.188 1284 Planarity : 0.004 0.031 1422 Dihedral : 10.203 106.390 1266 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.03 % Allowed : 27.29 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 30.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.26), residues: 1044 helix: 1.03 (0.25), residues: 438 sheet: -0.73 (0.44), residues: 140 loop : -1.17 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 460 HIS 0.003 0.001 HIS C 435 PHE 0.013 0.001 PHE C 667 TYR 0.018 0.002 TYR B 673 ARG 0.002 0.000 ARG D 628 Details of bonding type rmsd hydrogen bonds : bond 0.03485 ( 328) hydrogen bonds : angle 4.62372 ( 945) SS BOND : bond 0.00293 ( 4) SS BOND : angle 0.74343 ( 8) covalent geometry : bond 0.00386 ( 8538) covalent geometry : angle 0.58825 (11520) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: B 411 ASN cc_start: 0.7063 (p0) cc_final: 0.6693 (p0) REVERT: B 466 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6464 (tt0) REVERT: B 476 ILE cc_start: 0.8871 (mp) cc_final: 0.8574 (mt) REVERT: C 498 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8406 (pp) REVERT: C 697 LYS cc_start: 0.8359 (mttp) cc_final: 0.7284 (tptp) REVERT: C 704 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7831 (pt) REVERT: C 705 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7469 (mt-10) REVERT: D 442 LEU cc_start: 0.8418 (mt) cc_final: 0.8172 (mp) REVERT: D 453 ARG cc_start: 0.7387 (ttt90) cc_final: 0.7073 (ttm-80) REVERT: D 684 ARG cc_start: 0.7347 (tpp80) cc_final: 0.7087 (tpt-90) outliers start: 36 outliers final: 28 residues processed: 188 average time/residue: 0.2167 time to fit residues: 54.1741 Evaluate side-chains 181 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 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 466 GLU Chi-restraints excluded: chain B residue 467 LEU 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 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 712 ILE 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 484 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.0980 chunk 88 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.4115 r_free = 0.4115 target = 0.168371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.146533 restraints weight = 14026.648| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.88 r_work: 0.3746 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8542 Z= 0.107 Angle : 0.548 7.698 11528 Z= 0.278 Chirality : 0.043 0.171 1284 Planarity : 0.003 0.030 1422 Dihedral : 9.509 98.572 1266 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.47 % Allowed : 27.96 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 30.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.26), residues: 1044 helix: 1.12 (0.25), residues: 440 sheet: -0.55 (0.42), residues: 152 loop : -1.33 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 460 HIS 0.002 0.001 HIS B 435 PHE 0.006 0.001 PHE C 495 TYR 0.016 0.001 TYR B 673 ARG 0.001 0.000 ARG B 684 Details of bonding type rmsd hydrogen bonds : bond 0.02896 ( 328) hydrogen bonds : angle 4.50671 ( 945) SS BOND : bond 0.00143 ( 4) SS BOND : angle 0.50498 ( 8) covalent geometry : bond 0.00247 ( 8538) covalent geometry : angle 0.54792 (11520) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: A 756 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.7197 (pt0) REVERT: B 411 ASN cc_start: 0.7118 (p0) cc_final: 0.6750 (p0) REVERT: B 453 ARG cc_start: 0.6580 (OUTLIER) cc_final: 0.5761 (tmm-80) REVERT: B 476 ILE cc_start: 0.8853 (mp) cc_final: 0.8569 (mt) REVERT: B 661 ARG cc_start: 0.7419 (tpm170) cc_final: 0.6967 (mtp85) REVERT: B 688 GLU cc_start: 0.8348 (tp30) cc_final: 0.8001 (tp30) REVERT: C 498 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8393 (pp) REVERT: C 697 LYS cc_start: 0.8412 (mttp) cc_final: 0.7260 (tptp) REVERT: C 704 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7802 (pt) REVERT: C 705 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7400 (mt-10) REVERT: D 453 ARG cc_start: 0.7299 (ttt90) cc_final: 0.6977 (ttm-80) REVERT: D 661 ARG cc_start: 0.7574 (tpm170) cc_final: 0.7337 (tpm170) REVERT: D 684 ARG cc_start: 0.7350 (tpp80) cc_final: 0.7100 (tpt-90) REVERT: D 715 ARG cc_start: 0.7395 (ttm-80) cc_final: 0.7130 (mpt180) REVERT: D 719 ASP cc_start: 0.7523 (p0) cc_final: 0.7179 (p0) REVERT: D 755 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7213 (tp30) outliers start: 31 outliers final: 21 residues processed: 181 average time/residue: 0.2227 time to fit residues: 53.1400 Evaluate side-chains 179 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 756 GLN 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 453 ARG 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 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 432 ILE Chi-restraints excluded: chain D residue 443 THR 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 Chi-restraints excluded: chain D residue 755 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 65 optimal weight: 0.1980 chunk 58 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 100 optimal weight: 0.3980 chunk 59 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** C 714 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.169461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.147831 restraints weight = 13812.391| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.83 r_work: 0.3761 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8542 Z= 0.105 Angle : 0.547 8.974 11528 Z= 0.275 Chirality : 0.043 0.174 1284 Planarity : 0.003 0.028 1422 Dihedral : 9.095 96.840 1266 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.36 % Allowed : 28.64 % Favored : 68.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 30.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.26), residues: 1044 helix: 1.20 (0.25), residues: 440 sheet: -0.62 (0.41), residues: 156 loop : -1.30 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 460 HIS 0.002 0.001 HIS C 412 PHE 0.006 0.001 PHE C 495 TYR 0.016 0.001 TYR B 673 ARG 0.002 0.000 ARG B 684 Details of bonding type rmsd hydrogen bonds : bond 0.02750 ( 328) hydrogen bonds : angle 4.44427 ( 945) SS BOND : bond 0.00106 ( 4) SS BOND : angle 0.38909 ( 8) covalent geometry : bond 0.00243 ( 8538) covalent geometry : angle 0.54722 (11520) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: A 697 LYS cc_start: 0.8484 (mttp) cc_final: 0.7265 (tptp) REVERT: B 411 ASN cc_start: 0.7085 (p0) cc_final: 0.6710 (p0) REVERT: B 453 ARG cc_start: 0.6560 (OUTLIER) cc_final: 0.5696 (tmm-80) REVERT: B 476 ILE cc_start: 0.8843 (mp) cc_final: 0.8563 (mt) REVERT: B 661 ARG cc_start: 0.7302 (tpm170) cc_final: 0.6967 (mtp85) REVERT: B 688 GLU cc_start: 0.8368 (tp30) cc_final: 0.8077 (tp30) REVERT: C 498 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8413 (pp) REVERT: C 697 LYS cc_start: 0.8405 (mttp) cc_final: 0.7281 (tptp) REVERT: C 704 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7817 (pt) REVERT: C 705 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7415 (mt-10) REVERT: D 453 ARG cc_start: 0.7328 (ttt90) cc_final: 0.7019 (ttm-80) REVERT: D 661 ARG cc_start: 0.7503 (tpm170) cc_final: 0.7171 (mtp85) REVERT: D 684 ARG cc_start: 0.7386 (tpp80) cc_final: 0.7111 (tpt-90) REVERT: D 715 ARG cc_start: 0.7381 (ttm-80) cc_final: 0.7129 (mpt180) REVERT: D 719 ASP cc_start: 0.7388 (p0) cc_final: 0.7047 (p0) outliers start: 30 outliers final: 23 residues processed: 178 average time/residue: 0.2388 time to fit residues: 55.8482 Evaluate side-chains 184 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 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 453 ARG 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 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 432 ILE 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 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 6 optimal weight: 5.9990 chunk 49 optimal weight: 0.0970 chunk 17 optimal weight: 0.4980 chunk 3 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 chunk 71 optimal weight: 0.4980 chunk 105 optimal weight: 0.0670 overall best weight: 0.3516 ------------------------------------------------------------------------------- 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 = 0.4137 r_free = 0.4137 target = 0.170378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.148834 restraints weight = 13909.998| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.79 r_work: 0.3776 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8542 Z= 0.100 Angle : 0.546 9.507 11528 Z= 0.274 Chirality : 0.042 0.170 1284 Planarity : 0.003 0.029 1422 Dihedral : 8.934 95.449 1266 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.02 % Allowed : 29.08 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 30.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.26), residues: 1044 helix: 1.20 (0.25), residues: 440 sheet: -0.61 (0.41), residues: 156 loop : -1.29 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 766 HIS 0.001 0.001 HIS C 412 PHE 0.006 0.001 PHE C 495 TYR 0.012 0.001 TYR B 673 ARG 0.002 0.000 ARG C 661 Details of bonding type rmsd hydrogen bonds : bond 0.02695 ( 328) hydrogen bonds : angle 4.44548 ( 945) SS BOND : bond 0.00083 ( 4) SS BOND : angle 0.36294 ( 8) covalent geometry : bond 0.00224 ( 8538) covalent geometry : angle 0.54610 (11520) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3705.51 seconds wall clock time: 65 minutes 12.93 seconds (3912.93 seconds total)