Starting phenix.real_space_refine on Sat Jun 7 03:42:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fqa_29381/06_2025/8fqa_29381.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fqa_29381/06_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_29381/06_2025/8fqa_29381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fqa_29381/06_2025/8fqa_29381.map" model { file = "/net/cci-nas-00/data/ceres_data/8fqa_29381/06_2025/8fqa_29381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fqa_29381/06_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 6.07, per 1000 atoms: 0.72 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 954.3 milliseconds 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 23 sheets defined 42.7% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 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: 2.11 Time building geometry restraints manager: 2.47 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: 3.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.500 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.510 ------------------------------------------------------------------------------- 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 : 0.970 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 172 average time/residue: 0.2464 time to fit residues: 55.2866 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 : 0.915 ------------------------------------------------------------------------------- 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 = 0.4128 r_free = 0.4128 target = 0.169540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.147834 restraints weight = 13756.141| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.85 r_work: 0.3766 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 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 : 0.873 Fit side-chains revert: symmetry clash REVERT: B 411 ASN cc_start: 0.7372 (p0) cc_final: 0.7146 (p0) REVERT: B 476 ILE cc_start: 0.8895 (mp) cc_final: 0.8611 (mt) REVERT: C 697 LYS cc_start: 0.8333 (mttp) cc_final: 0.7245 (tptp) REVERT: C 705 GLU cc_start: 0.7978 (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: 0.2400 time to fit residues: 60.7796 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 : 0.940 ------------------------------------------------------------------------------- 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: 0.0570 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: 7.9990 chunk 61 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 overall best weight: 0.9516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4119 r_free = 0.4119 target = 0.168899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.146914 restraints weight = 13968.678| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.88 r_work: 0.3757 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1386 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= 0.114 Angle : 0.526 7.241 11528 Z= 0.268 Chirality : 0.043 0.149 1284 Planarity : 0.004 0.053 1422 Dihedral : 10.204 99.538 1266 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.47 % Allowed : 25.95 % Favored : 70.58 % 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: -0.03 (0.26), residues: 1044 helix: 1.25 (0.25), residues: 440 sheet: -0.41 (0.41), residues: 156 loop : -1.14 (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 0.008 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 0.03049 ( 328) hydrogen bonds : angle 4.65248 ( 945) SS BOND : bond 0.00192 ( 4) SS BOND : angle 0.68972 ( 8) covalent geometry : bond 0.00264 ( 8538) covalent geometry : angle 0.52583 (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 213 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: A 674 MET cc_start: 0.8024 (mtm) cc_final: 0.7727 (mtp) REVERT: A 705 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7219 (mm-30) REVERT: B 411 ASN cc_start: 0.7329 (p0) cc_final: 0.6971 (p0) REVERT: B 476 ILE cc_start: 0.8865 (mp) cc_final: 0.8594 (mt) REVERT: B 688 GLU cc_start: 0.8414 (tp30) cc_final: 0.8149 (tp30) REVERT: C 697 LYS cc_start: 0.8361 (mttp) cc_final: 0.7254 (tptp) REVERT: C 705 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7243 (mt-10) REVERT: D 414 MET cc_start: 0.6232 (pmm) cc_final: 0.5750 (pmm) REVERT: D 453 ARG cc_start: 0.7379 (ttt90) cc_final: 0.6969 (ttm-80) REVERT: D 719 ASP cc_start: 0.7257 (p0) cc_final: 0.6949 (p0) REVERT: D 722 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8537 (tttp) outliers start: 31 outliers final: 16 residues processed: 199 average time/residue: 0.2379 time to fit residues: 62.6837 Evaluate side-chains 179 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 769 ASP Chi-restraints excluded: chain D residue 722 LYS 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: 0.5980 chunk 29 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.4116 r_free = 0.4116 target = 0.168621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.146901 restraints weight = 13922.299| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.80 r_work: 0.3754 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1615 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= 0.118 Angle : 0.530 6.690 11528 Z= 0.270 Chirality : 0.043 0.214 1284 Planarity : 0.004 0.037 1422 Dihedral : 9.770 99.555 1266 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.24 % Allowed : 26.96 % Favored : 69.80 % 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: -0.09 (0.26), residues: 1044 helix: 1.25 (0.25), residues: 440 sheet: -0.22 (0.43), residues: 132 loop : -1.29 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 766 HIS 0.003 0.001 HIS C 412 PHE 0.009 0.001 PHE C 667 TYR 0.016 0.001 TYR C 673 ARG 0.001 0.000 ARG B 628 Details of bonding type rmsd hydrogen bonds : bond 0.02974 ( 328) hydrogen bonds : angle 4.55764 ( 945) SS BOND : bond 0.00170 ( 4) SS BOND : angle 0.69217 ( 8) covalent geometry : bond 0.00274 ( 8538) covalent geometry : angle 0.52988 (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 202 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: B 411 ASN cc_start: 0.7296 (p0) cc_final: 0.6920 (p0) REVERT: B 476 ILE cc_start: 0.8831 (mp) cc_final: 0.8567 (mt) REVERT: B 688 GLU cc_start: 0.8397 (tp30) cc_final: 0.8098 (tp30) REVERT: C 697 LYS cc_start: 0.8319 (mttp) cc_final: 0.7242 (tptp) REVERT: C 704 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7741 (pt) REVERT: C 705 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7243 (mt-10) REVERT: D 414 MET cc_start: 0.6183 (pmm) cc_final: 0.5833 (pmm) REVERT: D 453 ARG cc_start: 0.7512 (ttt90) cc_final: 0.7126 (ttm-80) REVERT: D 713 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6975 (mt-10) REVERT: D 719 ASP cc_start: 0.7338 (p0) cc_final: 0.7013 (p0) REVERT: D 755 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6904 (tp30) outliers start: 29 outliers final: 19 residues processed: 193 average time/residue: 0.2387 time to fit residues: 60.6203 Evaluate side-chains 184 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 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: 0.8980 chunk 65 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 18 optimal weight: 0.0980 chunk 16 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4126 r_free = 0.4126 target = 0.169541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.147719 restraints weight = 13747.548| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.83 r_work: 0.3761 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1758 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= 0.102 Angle : 0.515 6.352 11528 Z= 0.262 Chirality : 0.042 0.157 1284 Planarity : 0.003 0.030 1422 Dihedral : 9.180 95.779 1266 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.69 % Allowed : 26.06 % Favored : 70.25 % 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: 0.01 (0.26), residues: 1044 helix: 1.32 (0.25), residues: 440 sheet: -0.43 (0.41), residues: 152 loop : -1.14 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 766 HIS 0.003 0.001 HIS C 412 PHE 0.006 0.001 PHE C 495 TYR 0.011 0.001 TYR D 702 ARG 0.001 0.000 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.02782 ( 328) hydrogen bonds : angle 4.47441 ( 945) SS BOND : bond 0.00145 ( 4) SS BOND : angle 0.59039 ( 8) covalent geometry : bond 0.00234 ( 8538) covalent geometry : angle 0.51507 (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 201 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 705 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7220 (mm-30) REVERT: B 411 ASN cc_start: 0.7325 (p0) cc_final: 0.6920 (p0) REVERT: B 476 ILE cc_start: 0.8831 (mp) cc_final: 0.8583 (mt) REVERT: B 661 ARG cc_start: 0.7366 (tpm170) cc_final: 0.6893 (mtp85) REVERT: B 688 GLU cc_start: 0.8397 (tp30) cc_final: 0.8096 (tp30) REVERT: C 498 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8112 (pp) REVERT: C 697 LYS cc_start: 0.8294 (mttp) cc_final: 0.7196 (tptp) REVERT: C 705 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7183 (mt-10) REVERT: D 453 ARG cc_start: 0.7442 (ttt90) cc_final: 0.7044 (ttm-80) REVERT: D 684 ARG cc_start: 0.7279 (tpp80) cc_final: 0.6998 (tpt-90) REVERT: D 713 GLU cc_start: 0.7289 (mt-10) cc_final: 0.7072 (mt-10) REVERT: D 755 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6939 (tp30) outliers start: 33 outliers final: 21 residues processed: 192 average time/residue: 0.2297 time to fit residues: 58.4676 Evaluate side-chains 183 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain C residue 408 MET 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 666 VAL Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 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: 5.9990 chunk 17 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 91 optimal weight: 0.0060 chunk 30 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 44 optimal weight: 0.2980 chunk 73 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 overall best weight: 2.4200 ------------------------------------------------------------------------------- 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 = 0.4078 r_free = 0.4078 target = 0.164671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.142714 restraints weight = 14127.072| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.80 r_work: 0.3704 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8542 Z= 0.209 Angle : 0.624 6.684 11528 Z= 0.323 Chirality : 0.047 0.178 1284 Planarity : 0.004 0.035 1422 Dihedral : 10.716 109.204 1266 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.59 % Allowed : 26.85 % 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: -0.33 (0.25), residues: 1044 helix: 1.01 (0.25), residues: 426 sheet: -0.67 (0.42), residues: 150 loop : -1.20 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 460 HIS 0.004 0.001 HIS C 412 PHE 0.019 0.002 PHE C 667 TYR 0.018 0.002 TYR A 424 ARG 0.003 0.000 ARG D 628 Details of bonding type rmsd hydrogen bonds : bond 0.03942 ( 328) hydrogen bonds : angle 4.80403 ( 945) SS BOND : bond 0.00469 ( 4) SS BOND : angle 1.05350 ( 8) covalent geometry : bond 0.00493 ( 8538) covalent geometry : angle 0.62402 (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 204 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 163 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: B 411 ASN cc_start: 0.7046 (p0) cc_final: 0.6379 (p0) REVERT: B 414 MET cc_start: 0.7209 (pmm) cc_final: 0.6396 (pmm) REVERT: C 498 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8466 (pp) REVERT: C 704 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7819 (pt) REVERT: C 705 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7552 (mt-10) REVERT: D 442 LEU cc_start: 0.8450 (mt) cc_final: 0.8194 (mp) REVERT: D 453 ARG cc_start: 0.7508 (ttt90) cc_final: 0.7166 (ttm-80) REVERT: D 496 MET cc_start: 0.8688 (ttt) cc_final: 0.8412 (ttt) REVERT: D 684 ARG cc_start: 0.7296 (tpp80) cc_final: 0.7021 (tpt-90) REVERT: D 728 ASP cc_start: 0.7702 (t0) cc_final: 0.7475 (t0) outliers start: 41 outliers final: 30 residues processed: 190 average time/residue: 0.2511 time to fit residues: 63.1544 Evaluate side-chains 185 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 666 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 769 ASP Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 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: 2.9990 chunk 17 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 6 optimal weight: 0.0070 chunk 82 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 91 optimal weight: 0.0770 chunk 57 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.6162 ------------------------------------------------------------------------------- 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 = 0.4089 r_free = 0.4089 target = 0.165708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.144190 restraints weight = 14159.717| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.75 r_work: 0.3728 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8542 Z= 0.154 Angle : 0.571 6.484 11528 Z= 0.293 Chirality : 0.045 0.166 1284 Planarity : 0.004 0.034 1422 Dihedral : 10.235 103.041 1266 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.03 % Allowed : 28.08 % 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: -0.37 (0.25), residues: 1044 helix: 1.03 (0.26), residues: 426 sheet: -0.65 (0.46), residues: 120 loop : -1.27 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 460 HIS 0.002 0.001 HIS C 412 PHE 0.011 0.001 PHE C 667 TYR 0.015 0.001 TYR B 673 ARG 0.002 0.000 ARG D 628 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 328) hydrogen bonds : angle 4.72908 ( 945) SS BOND : bond 0.00275 ( 4) SS BOND : angle 0.82693 ( 8) covalent geometry : bond 0.00361 ( 8538) covalent geometry : angle 0.57105 (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 190 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: A 674 MET cc_start: 0.7878 (mtm) cc_final: 0.7672 (mtp) REVERT: B 411 ASN cc_start: 0.7026 (p0) cc_final: 0.6371 (p0) REVERT: B 414 MET cc_start: 0.7152 (pmm) cc_final: 0.6415 (pmm) REVERT: B 466 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6529 (tt0) REVERT: C 697 LYS cc_start: 0.8398 (mttp) cc_final: 0.7243 (tptp) REVERT: C 704 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7748 (pt) REVERT: C 705 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7456 (mt-10) REVERT: D 442 LEU cc_start: 0.8427 (mt) cc_final: 0.8167 (mp) REVERT: D 453 ARG cc_start: 0.7388 (ttt90) cc_final: 0.7053 (ttm-80) REVERT: D 684 ARG cc_start: 0.7301 (tpp80) cc_final: 0.7058 (tpt-90) REVERT: D 755 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6971 (tp30) outliers start: 36 outliers final: 28 residues processed: 178 average time/residue: 0.2534 time to fit residues: 59.4706 Evaluate side-chains 176 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR 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 666 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 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 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 684 ARG Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 484 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 13 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 94 optimal weight: 0.1980 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 91 optimal weight: 0.0770 chunk 75 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 overall best weight: 1.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN ** 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 = 0.4098 r_free = 0.4098 target = 0.166315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.144725 restraints weight = 14083.546| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.79 r_work: 0.3730 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8542 Z= 0.142 Angle : 0.567 6.566 11528 Z= 0.291 Chirality : 0.045 0.193 1284 Planarity : 0.004 0.033 1422 Dihedral : 10.229 104.737 1266 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.03 % Allowed : 27.52 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 30.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.40 (0.25), residues: 1044 helix: 0.95 (0.25), residues: 436 sheet: -0.78 (0.44), residues: 140 loop : -1.25 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 460 HIS 0.002 0.001 HIS C 412 PHE 0.009 0.001 PHE C 667 TYR 0.012 0.001 TYR B 673 ARG 0.002 0.000 ARG D 628 Details of bonding type rmsd hydrogen bonds : bond 0.03338 ( 328) hydrogen bonds : angle 4.68369 ( 945) SS BOND : bond 0.00238 ( 4) SS BOND : angle 0.69879 ( 8) covalent geometry : bond 0.00334 ( 8538) covalent geometry : angle 0.56721 (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 193 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: A 674 MET cc_start: 0.7816 (mtm) cc_final: 0.7611 (mtp) REVERT: B 411 ASN cc_start: 0.7003 (p0) cc_final: 0.6325 (p0) REVERT: B 414 MET cc_start: 0.7128 (pmm) cc_final: 0.6627 (pmm) REVERT: B 466 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6478 (tt0) REVERT: C 697 LYS cc_start: 0.8385 (mttp) cc_final: 0.7250 (tptp) REVERT: C 704 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7810 (pt) REVERT: C 705 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7404 (mt-10) REVERT: D 442 LEU cc_start: 0.8448 (mt) cc_final: 0.8179 (mp) REVERT: D 453 ARG cc_start: 0.7375 (ttt90) cc_final: 0.7068 (ttm-80) REVERT: D 684 ARG cc_start: 0.7312 (tpp80) cc_final: 0.7098 (tpt-90) REVERT: D 755 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6982 (tp30) outliers start: 36 outliers final: 29 residues processed: 183 average time/residue: 0.2278 time to fit residues: 55.2680 Evaluate side-chains 180 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR 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 666 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 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 504 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 684 ARG Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 467 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.0000 chunk 88 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- 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 = 0.4104 r_free = 0.4104 target = 0.166692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.145017 restraints weight = 14174.689| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.81 r_work: 0.3734 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2397 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= 0.135 Angle : 0.563 7.305 11528 Z= 0.289 Chirality : 0.044 0.167 1284 Planarity : 0.003 0.032 1422 Dihedral : 10.084 102.506 1266 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.03 % Allowed : 27.85 % Favored : 68.12 % 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: -0.41 (0.25), residues: 1044 helix: 0.96 (0.25), residues: 436 sheet: -0.74 (0.44), residues: 140 loop : -1.29 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 460 HIS 0.002 0.001 HIS C 412 PHE 0.009 0.001 PHE C 667 TYR 0.014 0.001 TYR B 673 ARG 0.002 0.000 ARG D 628 Details of bonding type rmsd hydrogen bonds : bond 0.03232 ( 328) hydrogen bonds : angle 4.65407 ( 945) SS BOND : bond 0.00201 ( 4) SS BOND : angle 0.69273 ( 8) covalent geometry : bond 0.00315 ( 8538) covalent geometry : angle 0.56314 (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 189 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 153 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: B 411 ASN cc_start: 0.7029 (p0) cc_final: 0.6349 (p0) REVERT: B 414 MET cc_start: 0.7084 (pmm) cc_final: 0.6678 (pmm) REVERT: B 466 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6459 (tt0) REVERT: C 697 LYS cc_start: 0.8289 (mttp) cc_final: 0.7165 (tptp) REVERT: C 704 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7799 (pt) REVERT: C 705 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7360 (mt-10) REVERT: D 442 LEU cc_start: 0.8419 (mt) cc_final: 0.8135 (mp) REVERT: D 453 ARG cc_start: 0.7355 (ttt90) cc_final: 0.7054 (ttm-80) REVERT: D 684 ARG cc_start: 0.7309 (tpp80) cc_final: 0.7105 (tpt-90) REVERT: D 755 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6972 (tp30) outliers start: 36 outliers final: 29 residues processed: 178 average time/residue: 0.2395 time to fit residues: 56.2937 Evaluate side-chains 177 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR 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 666 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 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 504 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 684 ARG Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 467 LEU 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: 2.9990 chunk 58 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.166558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.144969 restraints weight = 13974.557| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.79 r_work: 0.3734 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2448 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= 0.133 Angle : 0.563 7.893 11528 Z= 0.289 Chirality : 0.044 0.171 1284 Planarity : 0.003 0.032 1422 Dihedral : 10.063 102.485 1266 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.69 % Allowed : 28.30 % 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: -0.39 (0.25), residues: 1044 helix: 0.97 (0.25), residues: 436 sheet: -0.68 (0.45), residues: 140 loop : -1.30 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 460 HIS 0.002 0.001 HIS C 412 PHE 0.009 0.001 PHE C 667 TYR 0.016 0.001 TYR B 673 ARG 0.002 0.000 ARG B 684 Details of bonding type rmsd hydrogen bonds : bond 0.03183 ( 328) hydrogen bonds : angle 4.64418 ( 945) SS BOND : bond 0.00196 ( 4) SS BOND : angle 0.66887 ( 8) covalent geometry : bond 0.00310 ( 8538) covalent geometry : angle 0.56316 (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 184 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 2.408 Fit side-chains revert: symmetry clash REVERT: B 411 ASN cc_start: 0.7001 (p0) cc_final: 0.6322 (p0) REVERT: B 414 MET cc_start: 0.7072 (pmm) cc_final: 0.6737 (pmm) REVERT: B 661 ARG cc_start: 0.7526 (tpm170) cc_final: 0.6948 (ttm-80) REVERT: C 697 LYS cc_start: 0.8335 (mttp) cc_final: 0.7244 (tptp) REVERT: C 704 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7799 (pt) REVERT: C 705 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7372 (mt-10) REVERT: D 442 LEU cc_start: 0.8432 (mt) cc_final: 0.8144 (mp) REVERT: D 684 ARG cc_start: 0.7328 (tpp80) cc_final: 0.7126 (tpt-90) REVERT: D 755 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7004 (tp30) outliers start: 33 outliers final: 30 residues processed: 176 average time/residue: 0.2530 time to fit residues: 59.3059 Evaluate side-chains 181 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 666 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 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 504 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 684 ARG Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 467 LEU 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 6 optimal weight: 0.0570 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 0.0980 chunk 3 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 50 optimal weight: 0.4980 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 0.0770 chunk 105 optimal weight: 0.0670 overall best weight: 0.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 642 GLN ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 726 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 = 0.4152 r_free = 0.4152 target = 0.171847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.150665 restraints weight = 13965.125| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 2.81 r_work: 0.3803 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2458 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= 0.097 Angle : 0.548 8.717 11528 Z= 0.274 Chirality : 0.042 0.167 1284 Planarity : 0.003 0.033 1422 Dihedral : 8.373 83.558 1266 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.80 % Allowed : 29.98 % Favored : 67.23 % 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: -0.27 (0.26), residues: 1044 helix: 1.13 (0.25), residues: 440 sheet: -0.45 (0.42), residues: 152 loop : -1.39 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 766 HIS 0.001 0.000 HIS C 412 PHE 0.006 0.001 PHE C 495 TYR 0.014 0.001 TYR A 673 ARG 0.003 0.000 ARG D 420 Details of bonding type rmsd hydrogen bonds : bond 0.02483 ( 328) hydrogen bonds : angle 4.50712 ( 945) SS BOND : bond 0.00053 ( 4) SS BOND : angle 0.26999 ( 8) covalent geometry : bond 0.00215 ( 8538) covalent geometry : angle 0.54812 (11520) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4049.78 seconds wall clock time: 71 minutes 18.49 seconds (4278.49 seconds total)