Starting phenix.real_space_refine on Thu Jul 2 20:29:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oaa_70277/07_2026/9oaa_70277.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oaa_70277/07_2026/9oaa_70277.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oaa_70277/07_2026/9oaa_70277.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oaa_70277/07_2026/9oaa_70277.map" model { file = "/net/cci-nas-00/data/ceres_data/9oaa_70277/07_2026/9oaa_70277.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oaa_70277/07_2026/9oaa_70277.cif" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.037 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: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 Zn 1 6.06 5 S 27 5.16 5 C 6283 2.51 5 N 1730 2.21 5 O 1883 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9929 Number of models: 1 Model: "" Number of chains: 9 Chain: "T" Number of atoms: 6843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 6843 Classifications: {'peptide': 858} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 27, 'TRANS': 830} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 708 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 86, 699 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Conformer: "B" Number of residues, atoms: 86, 699 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} bond proxies already assigned to first conformer: 701 Chain: "B" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 859 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 100} Chain: "C" Number of atoms: 727 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 89, 725 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Conformer: "B" Number of residues, atoms: 89, 725 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} bond proxies already assigned to first conformer: 732 Chain: "D" Number of atoms: 786 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 95, 778 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 93} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 95, 778 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 93} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 781 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 1 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AGLN A 69 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 69 " occ=0.50 residue: pdb=" N AMET D 81 " occ=0.70 ... (14 atoms not shown) pdb=" CE BMET D 81 " occ=0.30 Time building chain proxies: 2.56, per 1000 atoms: 0.26 Number of scatterers: 9929 At special positions: 0 Unit cell: (69.564, 95.914, 133.858, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Ca 5 19.99 S 27 16.00 O 1883 8.00 N 1730 7.00 C 6283 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS T 554 " - pdb=" SG CYS T 558 " distance=2.03 Simple disulfide: pdb=" SG CYS T 886 " - pdb=" SG CYS T 893 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 429.4 milliseconds 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2260 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 11 sheets defined 28.4% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'T' and resid 55 through 59 Processing helix chain 'T' and resid 68 through 72 removed outlier: 3.624A pdb=" N SER T 72 " --> pdb=" O VAL T 69 " (cutoff:3.500A) Processing helix chain 'T' and resid 75 through 83 removed outlier: 3.548A pdb=" N VAL T 80 " --> pdb=" O LEU T 76 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ARG T 81 " --> pdb=" O ASP T 77 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER T 82 " --> pdb=" O ASN T 78 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE T 83 " --> pdb=" O ILE T 79 " (cutoff:3.500A) Processing helix chain 'T' and resid 175 through 180 removed outlier: 3.716A pdb=" N VAL T 179 " --> pdb=" O GLY T 175 " (cutoff:3.500A) Processing helix chain 'T' and resid 246 through 251 removed outlier: 4.374A pdb=" N TYR T 250 " --> pdb=" O PHE T 246 " (cutoff:3.500A) Processing helix chain 'T' and resid 255 through 262 removed outlier: 3.698A pdb=" N PHE T 259 " --> pdb=" O LYS T 255 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL T 260 " --> pdb=" O GLN T 256 " (cutoff:3.500A) Processing helix chain 'T' and resid 287 through 292 removed outlier: 3.875A pdb=" N GLU T 292 " --> pdb=" O TYR T 288 " (cutoff:3.500A) Processing helix chain 'T' and resid 293 through 312 removed outlier: 3.971A pdb=" N LEU T 297 " --> pdb=" O ASP T 293 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS T 299 " --> pdb=" O GLN T 295 " (cutoff:3.500A) Processing helix chain 'T' and resid 468 through 472 Processing helix chain 'T' and resid 602 through 607 Processing helix chain 'T' and resid 676 through 682 Processing helix chain 'T' and resid 866 through 870 removed outlier: 3.536A pdb=" N GLN T 869 " --> pdb=" O ALA T 866 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG T 870 " --> pdb=" O ALA T 867 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 866 through 870' Processing helix chain 'A' and resid 3 through 19 removed outlier: 3.546A pdb=" N ILE A 13 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR A 16 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N HIS A 17 " --> pdb=" O ILE A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 41 Processing helix chain 'A' and resid 43 through 48 Processing helix chain 'A' and resid 50 through 59 Processing helix chain 'A' and resid 67 through 86 Processing helix chain 'B' and resid 6 through 24 removed outlier: 3.676A pdb=" N TYR B 22 " --> pdb=" O THR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 44 Processing helix chain 'B' and resid 55 through 67 removed outlier: 3.766A pdb=" N ILE B 59 " --> pdb=" O ASN B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 78 Processing helix chain 'B' and resid 79 through 96 Processing helix chain 'C' and resid 3 through 17 Processing helix chain 'C' and resid 31 through 41 Processing helix chain 'C' and resid 43 through 48 Processing helix chain 'C' and resid 50 through 59 Processing helix chain 'C' and resid 67 through 87 Processing helix chain 'D' and resid 6 through 24 removed outlier: 3.676A pdb=" N TYR D 22 " --> pdb=" O THR D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 45 Processing helix chain 'D' and resid 55 through 67 removed outlier: 3.765A pdb=" N ILE D 59 " --> pdb=" O ASN D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 78 Processing helix chain 'D' and resid 79 through 98 removed outlier: 3.591A pdb=" N SER D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU D 92 " --> pdb=" O TRP D 88 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS D 93 " --> pdb=" O ALA D 89 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'T' and resid 62 through 66 removed outlier: 4.377A pdb=" N ALA T 62 " --> pdb=" O LYS T 153 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS T 153 " --> pdb=" O ALA T 62 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY T 148 " --> pdb=" O ARG T 172 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N MET T 113 " --> pdb=" O LEU T 171 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N THR T 173 " --> pdb=" O MET T 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'T' and resid 87 through 88 removed outlier: 4.046A pdb=" N SER T 98 " --> pdb=" O THR T 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'T' and resid 123 through 124 removed outlier: 3.659A pdb=" N SER T 123 " --> pdb=" O GLN T 136 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN T 136 " --> pdb=" O SER T 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'T' and resid 389 through 391 removed outlier: 4.002A pdb=" N ARG T 365 " --> pdb=" O SER T 389 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN T 368 " --> pdb=" O GLN T 349 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N MET T 204 " --> pdb=" O LYS T 191 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY T 192 " --> pdb=" O MET T 918 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA T 781 " --> pdb=" O ASP T 831 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR T 777 " --> pdb=" O ALA T 835 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL T 767 " --> pdb=" O GLY T 780 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR T 762 " --> pdb=" O ALA T 720 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG T 764 " --> pdb=" O SER T 718 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE T 702 " --> pdb=" O TYR T 721 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP T 628 " --> pdb=" O ARG T 654 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE T 580 " --> pdb=" O ALA T 592 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER T 577 " --> pdb=" O SER T 517 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS T 508 " --> pdb=" O GLU T 433 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU T 433 " --> pdb=" O LYS T 508 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR T 432 " --> pdb=" O LEU T 428 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE T 426 " --> pdb=" O LEU T 434 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'T' and resid 389 through 391 removed outlier: 4.002A pdb=" N ARG T 365 " --> pdb=" O SER T 389 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR T 432 " --> pdb=" O LEU T 428 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE T 426 " --> pdb=" O LEU T 434 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'T' and resid 399 through 400 removed outlier: 3.746A pdb=" N TRP T 403 " --> pdb=" O PHE T 400 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'T' and resid 524 through 530 removed outlier: 3.731A pdb=" N GLY T 569 " --> pdb=" O PHE T 525 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS T 567 " --> pdb=" O GLY T 527 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'T' and resid 661 through 663 Processing sheet with id=AA9, first strand: chain 'T' and resid 790 through 797 removed outlier: 4.629A pdb=" N GLN T 819 " --> pdb=" O THR T 792 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N GLU T 794 " --> pdb=" O ILE T 817 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE T 817 " --> pdb=" O GLU T 794 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 29 through 30 Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 30 379 hydrogen bonds defined for protein. 1046 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.65 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1801 1.32 - 1.45: 2752 1.45 - 1.57: 5536 1.57 - 1.69: 3 1.69 - 1.81: 50 Bond restraints: 10142 Sorted by residual: bond pdb=" CA HIS B 104 " pdb=" C HIS B 104 " ideal model delta sigma weight residual 1.521 1.679 -0.158 1.24e-02 6.50e+03 1.61e+02 bond pdb=" N HIS B 104 " pdb=" CA HIS B 104 " ideal model delta sigma weight residual 1.455 1.556 -0.101 1.25e-02 6.40e+03 6.59e+01 bond pdb=" N TYR A 16 " pdb=" CA TYR A 16 " ideal model delta sigma weight residual 1.457 1.562 -0.104 1.29e-02 6.01e+03 6.52e+01 bond pdb=" CA HIS B 95 " pdb=" C HIS B 95 " ideal model delta sigma weight residual 1.522 1.445 0.077 1.40e-02 5.10e+03 3.03e+01 bond pdb=" C ALA D 89 " pdb=" O ALA D 89 " ideal model delta sigma weight residual 1.236 1.294 -0.058 1.16e-02 7.43e+03 2.53e+01 ... (remaining 10137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.00: 13620 6.00 - 12.01: 34 12.01 - 18.01: 3 18.01 - 24.02: 0 24.02 - 30.02: 2 Bond angle restraints: 13659 Sorted by residual: angle pdb=" CG ASP C 14 " pdb=" CB ASP C 14 " pdb=" CA AASP C 14 " ideal model delta sigma weight residual 112.60 142.62 -30.02 1.00e+00 1.00e+00 9.01e+02 angle pdb=" CG ASP C 14 " pdb=" CB ASP C 14 " pdb=" CA BASP C 14 " ideal model delta sigma weight residual 112.60 142.61 -30.01 1.00e+00 1.00e+00 9.00e+02 angle pdb=" N PHE A 26 " pdb=" CA PHE A 26 " pdb=" CB PHE A 26 " ideal model delta sigma weight residual 110.22 93.99 16.23 1.54e+00 4.22e-01 1.11e+02 angle pdb=" O VAL A 15 " pdb=" C VAL A 15 " pdb=" N TYR A 16 " ideal model delta sigma weight residual 121.80 110.87 10.93 1.13e+00 7.83e-01 9.36e+01 angle pdb=" N MET D 94 " pdb=" CA MET D 94 " pdb=" C MET D 94 " ideal model delta sigma weight residual 112.54 101.20 11.34 1.22e+00 6.72e-01 8.64e+01 ... (remaining 13654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 5104 17.37 - 34.74: 686 34.74 - 52.11: 205 52.11 - 69.48: 35 69.48 - 86.85: 15 Dihedral angle restraints: 6045 sinusoidal: 2487 harmonic: 3558 Sorted by residual: dihedral pdb=" CA GLY B 100 " pdb=" C GLY B 100 " pdb=" N PRO B 101 " pdb=" CA PRO B 101 " ideal model delta harmonic sigma weight residual 0.00 -33.94 33.94 0 5.00e+00 4.00e-02 4.61e+01 dihedral pdb=" N PHE A 26 " pdb=" C PHE A 26 " pdb=" CA PHE A 26 " pdb=" CB PHE A 26 " ideal model delta harmonic sigma weight residual 122.80 106.65 16.15 0 2.50e+00 1.60e-01 4.17e+01 dihedral pdb=" CA LYS T 641 " pdb=" C LYS T 641 " pdb=" N GLN T 642 " pdb=" CA GLN T 642 " ideal model delta harmonic sigma weight residual 180.00 -150.85 -29.15 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 6042 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1288 0.074 - 0.149: 108 0.149 - 0.223: 15 0.223 - 0.297: 3 0.297 - 0.371: 2 Chirality restraints: 1416 Sorted by residual: chirality pdb=" CA TYR A 16 " pdb=" N TYR A 16 " pdb=" C TYR A 16 " pdb=" CB TYR A 16 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CA VAL A 29 " pdb=" N VAL A 29 " pdb=" C VAL A 29 " pdb=" CB VAL A 29 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA ILE A 12 " pdb=" N ILE A 12 " pdb=" C ILE A 12 " pdb=" CB ILE A 12 " both_signs ideal model delta sigma weight residual False 2.43 2.14 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 1413 not shown) Planarity restraints: 1788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 93 " 0.023 2.00e-02 2.50e+03 4.64e-02 2.15e+01 pdb=" C LYS B 93 " -0.080 2.00e-02 2.50e+03 pdb=" O LYS B 93 " 0.030 2.00e-02 2.50e+03 pdb=" N MET B 94 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 90 " 0.021 2.00e-02 2.50e+03 4.27e-02 1.83e+01 pdb=" C SER D 90 " -0.074 2.00e-02 2.50e+03 pdb=" O SER D 90 " 0.027 2.00e-02 2.50e+03 pdb=" N HIS D 91 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 16 " 0.022 2.00e-02 2.50e+03 4.25e-02 1.80e+01 pdb=" C TYR A 16 " -0.073 2.00e-02 2.50e+03 pdb=" O TYR A 16 " 0.025 2.00e-02 2.50e+03 pdb=" N HIS A 17 " 0.027 2.00e-02 2.50e+03 ... (remaining 1785 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 615 2.71 - 3.26: 9890 3.26 - 3.81: 15584 3.81 - 4.35: 19313 4.35 - 4.90: 33149 Nonbonded interactions: 78551 Sorted by model distance: nonbonded pdb=" NE2 HIS B 103 " pdb="ZN ZN B 201 " model vdw 2.165 2.310 nonbonded pdb=" N TYR A 16 " pdb=" O TYR A 16 " model vdw 2.201 2.496 nonbonded pdb=" OG SER T 487 " pdb=" O ILE T 611 " model vdw 2.227 3.040 nonbonded pdb=" OG1 THR T 728 " pdb=" O LYS T 818 " model vdw 2.233 3.040 nonbonded pdb=" NE2 HIS B 91 " pdb="ZN ZN B 201 " model vdw 2.237 2.310 ... (remaining 78546 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 13 or resid 15 through 68 or resid 70 through 10 \ 1)) selection = (chain 'C' and (resid 1 through 13 or resid 15 through 68 or resid 70 through 86 \ or resid 101)) } ncs_group { reference = (chain 'B' and (resid 4 through 80 or resid 82 through 92 or (resid 93 and (name \ N or name CA or name C or name O or name CB )) or resid 94 through 95 or (resid \ 96 and (name N or name CA or name C or name O or name CB )) or resid 97 or (res \ id 98 and (name N or name CA or name C or name O or name CB )) or resid 203)) selection = (chain 'D' and (resid 4 through 80 or resid 82 through 201)) } 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=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.100 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.870 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 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 : 0.005 0.158 10144 Z= 0.380 Angle : 0.915 30.021 13663 Z= 0.649 Chirality : 0.048 0.371 1416 Planarity : 0.004 0.052 1788 Dihedral : 17.464 86.854 3779 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.90 % Allowed : 13.96 % Favored : 85.14 % Rotamer: Outliers : 6.46 % Allowed : 16.52 % Favored : 77.02 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.43 (0.23), residues: 1227 helix: -0.48 (0.30), residues: 303 sheet: -2.62 (0.27), residues: 316 loop : -3.07 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 10 TYR 0.025 0.001 TYR A 16 PHE 0.030 0.001 PHE D 79 TRP 0.009 0.001 TRP D 88 HIS 0.014 0.001 HIS B 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.38 (10142) covalent geometry : angle 0.91525 / 0.65 (13659) SS BOND : bond 0.00043 / 0.02 ( 2) SS BOND : angle 0.49488 / 0.19 ( 4) hydrogen bonds : bond 0.23424 / 15.40 ( 372) hydrogen bonds : angle 9.97948 / 6.92 ( 1046) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 249 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: T 92 LYS cc_start: 0.8101 (mttm) cc_final: 0.7861 (mttm) REVERT: T 97 VAL cc_start: 0.8293 (OUTLIER) cc_final: 0.8026 (m) REVERT: T 190 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8074 (mt) REVERT: T 275 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7867 (pm20) REVERT: T 361 LYS cc_start: 0.7613 (ttpt) cc_final: 0.6896 (mtmm) REVERT: T 408 ASP cc_start: 0.7881 (m-30) cc_final: 0.7505 (m-30) REVERT: T 744 ASP cc_start: 0.7970 (t70) cc_final: 0.7686 (t0) REVERT: T 918 MET cc_start: 0.8102 (ttt) cc_final: 0.7812 (ttt) REVERT: A 16 TYR cc_start: 0.7907 (t80) cc_final: 0.7579 (t80) REVERT: B 83 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.6908 (mmt) REVERT: C 7 LYS cc_start: 0.8771 (mtmt) cc_final: 0.8552 (mttm) REVERT: C 49 LYS cc_start: 0.8160 (ttmt) cc_final: 0.7851 (ttmt) outliers start: 65 outliers final: 17 residues processed: 294 average time/residue: 0.1109 time to fit residues: 44.5185 Evaluate side-chains 200 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 97 VAL Chi-restraints excluded: chain T residue 120 THR Chi-restraints excluded: chain T residue 165 LEU Chi-restraints excluded: chain T residue 190 LEU Chi-restraints excluded: chain T residue 275 GLU Chi-restraints excluded: chain T residue 362 ILE Chi-restraints excluded: chain T residue 379 THR Chi-restraints excluded: chain T residue 459 PHE Chi-restraints excluded: chain T residue 488 THR Chi-restraints excluded: chain T residue 490 VAL Chi-restraints excluded: chain T residue 597 THR Chi-restraints excluded: chain T residue 663 ASN Chi-restraints excluded: chain T residue 767 VAL Chi-restraints excluded: chain T residue 848 VAL Chi-restraints excluded: chain T residue 913 THR Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain D residue 88 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... T 304 HIS T 413 ASN T 515 ASN T 629 GLN T 748 GLN T 826 GLN A 69 GLN A B 34 GLN ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.143394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.117686 restraints weight = 40398.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.122745 restraints weight = 32734.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.126786 restraints weight = 10455.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.130075 restraints weight = 6314.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.130476 restraints weight = 4237.410| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (5 function evaluations) r_final: 0.3439 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10144 Z= 0.204 Angle : 0.706 9.202 13663 Z= 0.372 Chirality : 0.045 0.235 1416 Planarity : 0.005 0.052 1788 Dihedral : 7.252 58.760 1398 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.86 % Favored : 84.98 % Rotamer: Outliers : 5.03 % Allowed : 19.66 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.36 (0.23), residues: 1227 helix: -0.37 (0.28), residues: 345 sheet: -2.56 (0.26), residues: 353 loop : -3.23 (0.24), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 42 TYR 0.022 0.002 TYR T 394 PHE 0.024 0.002 PHE T 156 TRP 0.011 0.001 TRP T 678 HIS 0.009 0.001 HIS A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 (10142) covalent geometry : angle 0.70564 / 0.37 (13659) SS BOND : bond 0.00073 / 0.04 ( 2) SS BOND : angle 0.85861 / 0.32 ( 4) hydrogen bonds : bond 0.04585 / 2.99 ( 372) hydrogen bonds : angle 5.94282 / 4.18 ( 1046) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 204 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 68 ASP cc_start: 0.6350 (OUTLIER) cc_final: 0.6081 (p0) REVERT: T 79 ILE cc_start: 0.8765 (mm) cc_final: 0.8544 (tt) REVERT: T 92 LYS cc_start: 0.8151 (mttm) cc_final: 0.7934 (mttm) REVERT: T 162 ILE cc_start: 0.8875 (tt) cc_final: 0.8654 (tt) REVERT: T 165 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7205 (mp) REVERT: T 304 HIS cc_start: 0.9160 (OUTLIER) cc_final: 0.8704 (t-90) REVERT: T 361 LYS cc_start: 0.7812 (ttpt) cc_final: 0.7383 (mttp) REVERT: T 732 ASP cc_start: 0.7110 (OUTLIER) cc_final: 0.6844 (p0) REVERT: B 51 LYS cc_start: 0.8778 (ttmm) cc_final: 0.8373 (mtpp) REVERT: B 90 SER cc_start: 0.9165 (m) cc_final: 0.8568 (t) REVERT: C 7 LYS cc_start: 0.8752 (mtmt) cc_final: 0.8552 (mttm) REVERT: D 94 MET cc_start: 0.6825 (mmm) cc_final: 0.6383 (mmm) outliers start: 51 outliers final: 29 residues processed: 246 average time/residue: 0.1014 time to fit residues: 35.0595 Evaluate side-chains 208 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 67 GLN Chi-restraints excluded: chain T residue 68 ASP Chi-restraints excluded: chain T residue 120 THR Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain T residue 165 LEU Chi-restraints excluded: chain T residue 176 VAL Chi-restraints excluded: chain T residue 197 ASN Chi-restraints excluded: chain T residue 234 TYR Chi-restraints excluded: chain T residue 304 HIS Chi-restraints excluded: chain T residue 319 THR Chi-restraints excluded: chain T residue 362 ILE Chi-restraints excluded: chain T residue 379 THR Chi-restraints excluded: chain T residue 417 ILE Chi-restraints excluded: chain T residue 423 THR Chi-restraints excluded: chain T residue 438 LEU Chi-restraints excluded: chain T residue 488 THR Chi-restraints excluded: chain T residue 490 VAL Chi-restraints excluded: chain T residue 597 THR Chi-restraints excluded: chain T residue 729 ASN Chi-restraints excluded: chain T residue 732 ASP Chi-restraints excluded: chain T residue 767 VAL Chi-restraints excluded: chain T residue 812 LEU Chi-restraints excluded: chain T residue 816 SER Chi-restraints excluded: chain T residue 848 VAL Chi-restraints excluded: chain T residue 913 THR Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 92 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 44 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... T 202 ASN ** T 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 413 ASN T 602 ASN T 626 ASN T 690 HIS ** A 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.135567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.109827 restraints weight = 35166.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.115499 restraints weight = 27659.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.117540 restraints weight = 10234.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.118486 restraints weight = 7748.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.119234 restraints weight = 6634.616| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 10144 Z= 0.269 Angle : 0.751 7.787 13663 Z= 0.398 Chirality : 0.046 0.215 1416 Planarity : 0.005 0.056 1788 Dihedral : 6.896 59.254 1376 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.19 % Favored : 84.65 % Rotamer: Outliers : 5.89 % Allowed : 19.75 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.36 (0.23), residues: 1227 helix: -0.33 (0.28), residues: 345 sheet: -2.61 (0.26), residues: 354 loop : -3.23 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 42 TYR 0.017 0.002 TYR T 394 PHE 0.018 0.002 PHE A 26 TRP 0.013 0.001 TRP T 287 HIS 0.020 0.002 HIS T 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00614 / 0.27 (10142) covalent geometry : angle 0.75069 / 0.40 (13659) SS BOND : bond 0.00801 / 0.38 ( 2) SS BOND : angle 1.75525 / 0.64 ( 4) hydrogen bonds : bond 0.04469 / 2.93 ( 372) hydrogen bonds : angle 5.72183 / 4.00 ( 1046) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 195 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 92 LYS cc_start: 0.8223 (mttm) cc_final: 0.7972 (mttm) REVERT: T 304 HIS cc_start: 0.9175 (OUTLIER) cc_final: 0.8856 (t70) REVERT: T 361 LYS cc_start: 0.7853 (ttpt) cc_final: 0.7332 (mttp) REVERT: T 477 LYS cc_start: 0.8637 (tptp) cc_final: 0.8358 (tptp) REVERT: T 480 LYS cc_start: 0.7213 (OUTLIER) cc_final: 0.6540 (mttp) REVERT: A 16 TYR cc_start: 0.8619 (t80) cc_final: 0.8367 (t80) REVERT: B 83 MET cc_start: 0.7994 (tpp) cc_final: 0.7750 (mmt) REVERT: B 90 SER cc_start: 0.9091 (m) cc_final: 0.8732 (t) REVERT: C 7 LYS cc_start: 0.8816 (mtmt) cc_final: 0.8611 (mttm) outliers start: 60 outliers final: 42 residues processed: 240 average time/residue: 0.1012 time to fit residues: 34.4589 Evaluate side-chains 220 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 176 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 69 VAL Chi-restraints excluded: chain T residue 120 THR Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain T residue 165 LEU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 194 THR Chi-restraints excluded: chain T residue 197 ASN Chi-restraints excluded: chain T residue 234 TYR Chi-restraints excluded: chain T residue 278 LEU Chi-restraints excluded: chain T residue 304 HIS Chi-restraints excluded: chain T residue 319 THR Chi-restraints excluded: chain T residue 362 ILE Chi-restraints excluded: chain T residue 379 THR Chi-restraints excluded: chain T residue 411 THR Chi-restraints excluded: chain T residue 417 ILE Chi-restraints excluded: chain T residue 480 LYS Chi-restraints excluded: chain T residue 488 THR Chi-restraints excluded: chain T residue 490 VAL Chi-restraints excluded: chain T residue 553 HIS Chi-restraints excluded: chain T residue 597 THR Chi-restraints excluded: chain T residue 614 SER Chi-restraints excluded: chain T residue 661 ILE Chi-restraints excluded: chain T residue 663 ASN Chi-restraints excluded: chain T residue 695 ASP Chi-restraints excluded: chain T residue 702 PHE Chi-restraints excluded: chain T residue 724 SER Chi-restraints excluded: chain T residue 767 VAL Chi-restraints excluded: chain T residue 776 LEU Chi-restraints excluded: chain T residue 812 LEU Chi-restraints excluded: chain T residue 848 VAL Chi-restraints excluded: chain T residue 913 THR Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 92 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 80 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... T 304 HIS T 413 ASN ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.142316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.117050 restraints weight = 42297.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.121897 restraints weight = 33636.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.125988 restraints weight = 11003.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.128746 restraints weight = 6601.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.129577 restraints weight = 4729.677| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3445 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3445 r_free = 0.3445 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3445 r_free = 0.3445 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3445 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10144 Z= 0.152 Angle : 0.671 7.366 13663 Z= 0.354 Chirality : 0.043 0.172 1416 Planarity : 0.004 0.054 1788 Dihedral : 6.615 55.956 1376 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.70 % Favored : 85.14 % Rotamer: Outliers : 5.22 % Allowed : 21.65 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.17 (0.23), residues: 1227 helix: -0.23 (0.28), residues: 346 sheet: -2.36 (0.27), residues: 342 loop : -3.20 (0.24), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 42 TYR 0.023 0.001 TYR T 387 PHE 0.016 0.002 PHE T 460 TRP 0.009 0.001 TRP T 678 HIS 0.009 0.001 HIS A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (10142) covalent geometry : angle 0.67099 / 0.35 (13659) SS BOND : bond 0.00095 / 0.05 ( 2) SS BOND : angle 1.45466 / 0.54 ( 4) hydrogen bonds : bond 0.03649 / 2.38 ( 372) hydrogen bonds : angle 5.28670 / 3.69 ( 1046) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 184 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 68 ASP cc_start: 0.6706 (OUTLIER) cc_final: 0.6431 (p0) REVERT: T 92 LYS cc_start: 0.8182 (mttm) cc_final: 0.7931 (mttm) REVERT: T 304 HIS cc_start: 0.9215 (OUTLIER) cc_final: 0.8475 (t70) REVERT: T 361 LYS cc_start: 0.7792 (ttpt) cc_final: 0.7327 (mttp) REVERT: T 732 ASP cc_start: 0.7155 (OUTLIER) cc_final: 0.6860 (p0) REVERT: A 11 SER cc_start: 0.9038 (OUTLIER) cc_final: 0.8779 (t) REVERT: C 7 LYS cc_start: 0.8769 (mtmt) cc_final: 0.8565 (mttm) REVERT: D 60 GLU cc_start: 0.7852 (tp30) cc_final: 0.7581 (tp30) outliers start: 53 outliers final: 35 residues processed: 226 average time/residue: 0.0998 time to fit residues: 32.0519 Evaluate side-chains 207 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 56 VAL Chi-restraints excluded: chain T residue 68 ASP Chi-restraints excluded: chain T residue 69 VAL Chi-restraints excluded: chain T residue 120 THR Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain T residue 165 LEU Chi-restraints excluded: chain T residue 197 ASN Chi-restraints excluded: chain T residue 234 TYR Chi-restraints excluded: chain T residue 278 LEU Chi-restraints excluded: chain T residue 304 HIS Chi-restraints excluded: chain T residue 319 THR Chi-restraints excluded: chain T residue 362 ILE Chi-restraints excluded: chain T residue 379 THR Chi-restraints excluded: chain T residue 417 ILE Chi-restraints excluded: chain T residue 460 PHE Chi-restraints excluded: chain T residue 488 THR Chi-restraints excluded: chain T residue 490 VAL Chi-restraints excluded: chain T residue 553 HIS Chi-restraints excluded: chain T residue 597 THR Chi-restraints excluded: chain T residue 614 SER Chi-restraints excluded: chain T residue 648 LEU Chi-restraints excluded: chain T residue 663 ASN Chi-restraints excluded: chain T residue 695 ASP Chi-restraints excluded: chain T residue 702 PHE Chi-restraints excluded: chain T residue 732 ASP Chi-restraints excluded: chain T residue 767 VAL Chi-restraints excluded: chain T residue 776 LEU Chi-restraints excluded: chain T residue 812 LEU Chi-restraints excluded: chain T residue 820 THR Chi-restraints excluded: chain T residue 843 ILE Chi-restraints excluded: chain T residue 848 VAL Chi-restraints excluded: chain T residue 913 THR Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain D residue 49 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 90 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... T 304 HIS ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 HIS C 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.140298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.114844 restraints weight = 44833.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.119276 restraints weight = 34146.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.123587 restraints weight = 11142.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.125691 restraints weight = 6383.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.126036 restraints weight = 5012.080| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3409 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3409 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10144 Z= 0.175 Angle : 0.674 7.318 13663 Z= 0.353 Chirality : 0.043 0.208 1416 Planarity : 0.004 0.055 1788 Dihedral : 6.644 51.260 1376 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.02 % Favored : 84.81 % Rotamer: Outliers : 5.60 % Allowed : 22.98 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.23), residues: 1227 helix: -0.22 (0.28), residues: 352 sheet: -2.32 (0.27), residues: 342 loop : -3.22 (0.24), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 31 TYR 0.013 0.001 TYR T 291 PHE 0.017 0.002 PHE T 460 TRP 0.009 0.001 TRP T 287 HIS 0.014 0.001 HIS T 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (10142) covalent geometry : angle 0.67351 / 0.35 (13659) SS BOND : bond 0.00089 / 0.04 ( 2) SS BOND : angle 1.28816 / 0.46 ( 4) hydrogen bonds : bond 0.03636 / 2.39 ( 372) hydrogen bonds : angle 5.22452 / 3.65 ( 1046) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 186 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 92 LYS cc_start: 0.8229 (mttm) cc_final: 0.7978 (mttm) REVERT: T 177 ASP cc_start: 0.7970 (m-30) cc_final: 0.7698 (m-30) REVERT: T 304 HIS cc_start: 0.9117 (OUTLIER) cc_final: 0.8390 (t70) REVERT: T 361 LYS cc_start: 0.7875 (ttpt) cc_final: 0.7310 (mttp) REVERT: T 480 LYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6779 (mttt) REVERT: T 561 TYR cc_start: 0.7536 (t80) cc_final: 0.7320 (t80) REVERT: T 630 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7633 (t80) REVERT: T 732 ASP cc_start: 0.7151 (OUTLIER) cc_final: 0.6852 (p0) REVERT: A 58 LEU cc_start: 0.9006 (tp) cc_final: 0.8744 (tp) REVERT: C 7 LYS cc_start: 0.8803 (mtmt) cc_final: 0.8591 (mttm) REVERT: C 17 HIS cc_start: 0.8970 (OUTLIER) cc_final: 0.8575 (m170) REVERT: D 38 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8663 (mtpp) REVERT: D 60 GLU cc_start: 0.7849 (tp30) cc_final: 0.7556 (tp30) outliers start: 57 outliers final: 41 residues processed: 228 average time/residue: 0.1010 time to fit residues: 32.5999 Evaluate side-chains 219 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 172 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 56 VAL Chi-restraints excluded: chain T residue 68 ASP Chi-restraints excluded: chain T residue 69 VAL Chi-restraints excluded: chain T residue 120 THR Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain T residue 165 LEU Chi-restraints excluded: chain T residue 179 VAL Chi-restraints excluded: chain T residue 194 THR Chi-restraints excluded: chain T residue 197 ASN Chi-restraints excluded: chain T residue 234 TYR Chi-restraints excluded: chain T residue 278 LEU Chi-restraints excluded: chain T residue 304 HIS Chi-restraints excluded: chain T residue 319 THR Chi-restraints excluded: chain T residue 362 ILE Chi-restraints excluded: chain T residue 379 THR Chi-restraints excluded: chain T residue 417 ILE Chi-restraints excluded: chain T residue 460 PHE Chi-restraints excluded: chain T residue 480 LYS Chi-restraints excluded: chain T residue 488 THR Chi-restraints excluded: chain T residue 553 HIS Chi-restraints excluded: chain T residue 597 THR Chi-restraints excluded: chain T residue 614 SER Chi-restraints excluded: chain T residue 630 PHE Chi-restraints excluded: chain T residue 648 LEU Chi-restraints excluded: chain T residue 663 ASN Chi-restraints excluded: chain T residue 695 ASP Chi-restraints excluded: chain T residue 702 PHE Chi-restraints excluded: chain T residue 732 ASP Chi-restraints excluded: chain T residue 767 VAL Chi-restraints excluded: chain T residue 776 LEU Chi-restraints excluded: chain T residue 812 LEU Chi-restraints excluded: chain T residue 820 THR Chi-restraints excluded: chain T residue 843 ILE Chi-restraints excluded: chain T residue 848 VAL Chi-restraints excluded: chain T residue 913 THR Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain C residue 17 HIS Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 38 LYS Chi-restraints excluded: chain D residue 49 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 24 optimal weight: 6.9990 chunk 109 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 73 optimal weight: 0.4980 chunk 58 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 113 optimal weight: 7.9990 chunk 119 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... T 304 HIS T 311 ASN C 25 ASN C 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.143494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.117154 restraints weight = 36932.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.123018 restraints weight = 28198.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.125703 restraints weight = 10038.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.127396 restraints weight = 7183.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.128187 restraints weight = 6013.034| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 10144 Z= 0.139 Angle : 0.662 7.254 13663 Z= 0.344 Chirality : 0.042 0.177 1416 Planarity : 0.004 0.052 1788 Dihedral : 6.510 46.273 1375 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.20 % Favored : 85.63 % Rotamer: Outliers : 5.51 % Allowed : 23.46 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.23), residues: 1227 helix: -0.15 (0.28), residues: 351 sheet: -2.26 (0.27), residues: 359 loop : -3.11 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 42 TYR 0.024 0.001 TYR T 387 PHE 0.013 0.001 PHE T 460 TRP 0.007 0.001 TRP T 287 HIS 0.008 0.001 HIS T 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (10142) covalent geometry : angle 0.66140 / 0.34 (13659) SS BOND : bond 0.00078 / 0.04 ( 2) SS BOND : angle 1.11060 / 0.40 ( 4) hydrogen bonds : bond 0.03358 / 2.21 ( 372) hydrogen bonds : angle 5.12578 / 3.58 ( 1046) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 186 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 68 ASP cc_start: 0.6734 (OUTLIER) cc_final: 0.6261 (p0) REVERT: T 92 LYS cc_start: 0.8228 (mttm) cc_final: 0.7963 (mttm) REVERT: T 196 THR cc_start: 0.8067 (m) cc_final: 0.7666 (m) REVERT: T 304 HIS cc_start: 0.9060 (OUTLIER) cc_final: 0.8220 (t70) REVERT: T 361 LYS cc_start: 0.7852 (ttpt) cc_final: 0.7275 (mttp) REVERT: T 480 LYS cc_start: 0.7070 (OUTLIER) cc_final: 0.6864 (mttt) REVERT: T 630 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.7507 (t80) REVERT: T 732 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6899 (p0) REVERT: C 7 LYS cc_start: 0.8788 (mtmt) cc_final: 0.8549 (mttm) REVERT: C 84 LYS cc_start: 0.8579 (mmmt) cc_final: 0.8250 (mtmt) REVERT: D 38 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8753 (mtpp) REVERT: D 60 GLU cc_start: 0.7858 (tp30) cc_final: 0.7596 (tp30) outliers start: 56 outliers final: 37 residues processed: 223 average time/residue: 0.1010 time to fit residues: 32.1456 Evaluate side-chains 215 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 56 VAL Chi-restraints excluded: chain T residue 68 ASP Chi-restraints excluded: chain T residue 69 VAL Chi-restraints excluded: chain T residue 120 THR Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain T residue 165 LEU Chi-restraints excluded: chain T residue 179 VAL Chi-restraints excluded: chain T residue 194 THR Chi-restraints excluded: chain T residue 234 TYR Chi-restraints excluded: chain T residue 304 HIS Chi-restraints excluded: chain T residue 319 THR Chi-restraints excluded: chain T residue 362 ILE Chi-restraints excluded: chain T residue 379 THR Chi-restraints excluded: chain T residue 417 ILE Chi-restraints excluded: chain T residue 460 PHE Chi-restraints excluded: chain T residue 480 LYS Chi-restraints excluded: chain T residue 488 THR Chi-restraints excluded: chain T residue 553 HIS Chi-restraints excluded: chain T residue 597 THR Chi-restraints excluded: chain T residue 614 SER Chi-restraints excluded: chain T residue 630 PHE Chi-restraints excluded: chain T residue 648 LEU Chi-restraints excluded: chain T residue 663 ASN Chi-restraints excluded: chain T residue 702 PHE Chi-restraints excluded: chain T residue 732 ASP Chi-restraints excluded: chain T residue 767 VAL Chi-restraints excluded: chain T residue 776 LEU Chi-restraints excluded: chain T residue 812 LEU Chi-restraints excluded: chain T residue 843 ILE Chi-restraints excluded: chain T residue 848 VAL Chi-restraints excluded: chain T residue 913 THR Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 38 LYS Chi-restraints excluded: chain D residue 49 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 22 optimal weight: 4.9990 chunk 96 optimal weight: 0.3980 chunk 41 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 304 HIS ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.143664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.118842 restraints weight = 28940.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.121400 restraints weight = 19519.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.122849 restraints weight = 13312.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.124875 restraints weight = 8266.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.125452 restraints weight = 6975.393| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 10144 Z= 0.140 Angle : 0.659 8.260 13663 Z= 0.342 Chirality : 0.043 0.185 1416 Planarity : 0.004 0.049 1788 Dihedral : 6.523 57.866 1375 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.70 % Favored : 85.14 % Rotamer: Outliers : 5.13 % Allowed : 24.31 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.24), residues: 1227 helix: -0.20 (0.28), residues: 351 sheet: -2.20 (0.27), residues: 357 loop : -3.06 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG T 691 TYR 0.012 0.001 TYR T 291 PHE 0.014 0.001 PHE T 460 TRP 0.009 0.001 TRP T 287 HIS 0.005 0.001 HIS T 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (10142) covalent geometry : angle 0.65883 / 0.34 (13659) SS BOND : bond 0.00057 / 0.03 ( 2) SS BOND : angle 1.00442 / 0.36 ( 4) hydrogen bonds : bond 0.03358 / 2.22 ( 372) hydrogen bonds : angle 5.05951 / 3.53 ( 1046) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 180 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 67 GLN cc_start: 0.6633 (OUTLIER) cc_final: 0.6418 (mm-40) REVERT: T 68 ASP cc_start: 0.6589 (OUTLIER) cc_final: 0.6308 (p0) REVERT: T 156 PHE cc_start: 0.6235 (t80) cc_final: 0.5935 (t80) REVERT: T 304 HIS cc_start: 0.8973 (OUTLIER) cc_final: 0.8652 (t70) REVERT: T 361 LYS cc_start: 0.7776 (ttpt) cc_final: 0.7323 (mttp) REVERT: T 480 LYS cc_start: 0.6762 (OUTLIER) cc_final: 0.6373 (mttt) REVERT: T 630 PHE cc_start: 0.7962 (OUTLIER) cc_final: 0.7523 (t80) REVERT: T 732 ASP cc_start: 0.7171 (OUTLIER) cc_final: 0.6825 (p0) REVERT: C 84 LYS cc_start: 0.8466 (mmmt) cc_final: 0.8255 (ttmt) REVERT: D 38 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8700 (mtpp) REVERT: D 42 ARG cc_start: 0.8279 (ttm-80) cc_final: 0.7848 (mtt-85) REVERT: D 52 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8091 (mp0) REVERT: D 60 GLU cc_start: 0.7715 (tp30) cc_final: 0.7434 (tp30) outliers start: 52 outliers final: 41 residues processed: 216 average time/residue: 0.0990 time to fit residues: 30.5800 Evaluate side-chains 206 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 158 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 56 VAL Chi-restraints excluded: chain T residue 67 GLN Chi-restraints excluded: chain T residue 68 ASP Chi-restraints excluded: chain T residue 69 VAL Chi-restraints excluded: chain T residue 120 THR Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain T residue 165 LEU Chi-restraints excluded: chain T residue 179 VAL Chi-restraints excluded: chain T residue 194 THR Chi-restraints excluded: chain T residue 197 ASN Chi-restraints excluded: chain T residue 234 TYR Chi-restraints excluded: chain T residue 304 HIS Chi-restraints excluded: chain T residue 319 THR Chi-restraints excluded: chain T residue 362 ILE Chi-restraints excluded: chain T residue 379 THR Chi-restraints excluded: chain T residue 417 ILE Chi-restraints excluded: chain T residue 459 PHE Chi-restraints excluded: chain T residue 460 PHE Chi-restraints excluded: chain T residue 480 LYS Chi-restraints excluded: chain T residue 488 THR Chi-restraints excluded: chain T residue 597 THR Chi-restraints excluded: chain T residue 614 SER Chi-restraints excluded: chain T residue 630 PHE Chi-restraints excluded: chain T residue 648 LEU Chi-restraints excluded: chain T residue 663 ASN Chi-restraints excluded: chain T residue 695 ASP Chi-restraints excluded: chain T residue 702 PHE Chi-restraints excluded: chain T residue 732 ASP Chi-restraints excluded: chain T residue 767 VAL Chi-restraints excluded: chain T residue 776 LEU Chi-restraints excluded: chain T residue 812 LEU Chi-restraints excluded: chain T residue 843 ILE Chi-restraints excluded: chain T residue 848 VAL Chi-restraints excluded: chain T residue 913 THR Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 38 LYS Chi-restraints excluded: chain D residue 49 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 47 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... T 90 GLN T 304 HIS ** B 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN C 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.140983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.115081 restraints weight = 33553.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.118876 restraints weight = 26127.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.121471 restraints weight = 12343.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.122524 restraints weight = 8238.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.123572 restraints weight = 6851.888| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3309 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3309 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 10144 Z= 0.175 Angle : 0.684 9.887 13663 Z= 0.357 Chirality : 0.044 0.208 1416 Planarity : 0.004 0.058 1788 Dihedral : 6.552 52.734 1375 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.45 % Favored : 85.39 % Rotamer: Outliers : 5.22 % Allowed : 24.79 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.23), residues: 1227 helix: -0.33 (0.27), residues: 355 sheet: -2.28 (0.27), residues: 364 loop : -3.02 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG T 109 TYR 0.025 0.001 TYR T 387 PHE 0.014 0.002 PHE T 460 TRP 0.010 0.001 TRP T 287 HIS 0.007 0.001 HIS T 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (10142) covalent geometry : angle 0.68419 / 0.36 (13659) SS BOND : bond 0.00062 / 0.03 ( 2) SS BOND : angle 1.01709 / 0.37 ( 4) hydrogen bonds : bond 0.03550 / 2.35 ( 372) hydrogen bonds : angle 5.11583 / 3.56 ( 1046) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 166 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 92 LYS cc_start: 0.8234 (mttm) cc_final: 0.8009 (mttm) REVERT: T 190 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8345 (tt) REVERT: T 304 HIS cc_start: 0.9048 (OUTLIER) cc_final: 0.8703 (t70) REVERT: T 361 LYS cc_start: 0.7841 (ttpt) cc_final: 0.7355 (mttp) REVERT: T 630 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.7585 (t80) REVERT: T 732 ASP cc_start: 0.7364 (OUTLIER) cc_final: 0.7009 (p0) REVERT: D 52 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8130 (mp0) REVERT: D 60 GLU cc_start: 0.7789 (tp30) cc_final: 0.7510 (tp30) outliers start: 53 outliers final: 44 residues processed: 202 average time/residue: 0.1013 time to fit residues: 29.4797 Evaluate side-chains 207 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 159 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 56 VAL Chi-restraints excluded: chain T residue 68 ASP Chi-restraints excluded: chain T residue 69 VAL Chi-restraints excluded: chain T residue 120 THR Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain T residue 165 LEU Chi-restraints excluded: chain T residue 179 VAL Chi-restraints excluded: chain T residue 190 LEU Chi-restraints excluded: chain T residue 194 THR Chi-restraints excluded: chain T residue 197 ASN Chi-restraints excluded: chain T residue 234 TYR Chi-restraints excluded: chain T residue 304 HIS Chi-restraints excluded: chain T residue 319 THR Chi-restraints excluded: chain T residue 362 ILE Chi-restraints excluded: chain T residue 379 THR Chi-restraints excluded: chain T residue 417 ILE Chi-restraints excluded: chain T residue 459 PHE Chi-restraints excluded: chain T residue 460 PHE Chi-restraints excluded: chain T residue 488 THR Chi-restraints excluded: chain T residue 553 HIS Chi-restraints excluded: chain T residue 597 THR Chi-restraints excluded: chain T residue 614 SER Chi-restraints excluded: chain T residue 630 PHE Chi-restraints excluded: chain T residue 648 LEU Chi-restraints excluded: chain T residue 695 ASP Chi-restraints excluded: chain T residue 702 PHE Chi-restraints excluded: chain T residue 732 ASP Chi-restraints excluded: chain T residue 767 VAL Chi-restraints excluded: chain T residue 776 LEU Chi-restraints excluded: chain T residue 812 LEU Chi-restraints excluded: chain T residue 820 THR Chi-restraints excluded: chain T residue 843 ILE Chi-restraints excluded: chain T residue 848 VAL Chi-restraints excluded: chain T residue 913 THR Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 49 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 105 optimal weight: 2.9990 chunk 26 optimal weight: 0.0270 chunk 96 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 74 optimal weight: 0.0980 chunk 80 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... T 90 GLN T 304 HIS T 726 GLN ** B 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN D 73 GLN ** D 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.145339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.118855 restraints weight = 36916.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.124875 restraints weight = 27241.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.127983 restraints weight = 9331.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.128272 restraints weight = 6736.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.131405 restraints weight = 6120.449| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10144 Z= 0.125 Angle : 0.662 8.189 13663 Z= 0.343 Chirality : 0.042 0.186 1416 Planarity : 0.004 0.057 1788 Dihedral : 6.313 48.390 1375 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.88 % Favored : 85.96 % Rotamer: Outliers : 4.46 % Allowed : 25.55 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.24), residues: 1227 helix: -0.32 (0.28), residues: 355 sheet: -2.08 (0.28), residues: 359 loop : -2.91 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG T 109 TYR 0.015 0.001 TYR T 502 PHE 0.013 0.001 PHE T 460 TRP 0.007 0.001 TRP T 287 HIS 0.011 0.001 HIS T 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (10142) covalent geometry : angle 0.66198 / 0.34 (13659) SS BOND : bond 0.00077 / 0.04 ( 2) SS BOND : angle 0.90691 / 0.33 ( 4) hydrogen bonds : bond 0.03279 / 2.17 ( 372) hydrogen bonds : angle 4.99668 / 3.47 ( 1046) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 176 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 67 GLN cc_start: 0.6654 (OUTLIER) cc_final: 0.6444 (mm-40) REVERT: T 68 ASP cc_start: 0.6474 (OUTLIER) cc_final: 0.6170 (p0) REVERT: T 92 LYS cc_start: 0.8195 (mttm) cc_final: 0.7978 (mttm) REVERT: T 156 PHE cc_start: 0.6212 (t80) cc_final: 0.5887 (t80) REVERT: T 304 HIS cc_start: 0.8945 (OUTLIER) cc_final: 0.8714 (t70) REVERT: T 361 LYS cc_start: 0.7794 (ttpt) cc_final: 0.7204 (mttp) REVERT: T 630 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7479 (t80) REVERT: T 732 ASP cc_start: 0.7143 (OUTLIER) cc_final: 0.6783 (p0) REVERT: A 7 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8432 (ttpp) REVERT: B 11 ASN cc_start: 0.7966 (t0) cc_final: 0.7734 (t0) REVERT: D 22 TYR cc_start: 0.8119 (m-80) cc_final: 0.7828 (m-80) REVERT: D 52 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7999 (mp0) REVERT: D 60 GLU cc_start: 0.7873 (tp30) cc_final: 0.7505 (tp30) outliers start: 45 outliers final: 35 residues processed: 207 average time/residue: 0.0985 time to fit residues: 29.0754 Evaluate side-chains 205 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 164 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 56 VAL Chi-restraints excluded: chain T residue 67 GLN Chi-restraints excluded: chain T residue 68 ASP Chi-restraints excluded: chain T residue 69 VAL Chi-restraints excluded: chain T residue 120 THR Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain T residue 165 LEU Chi-restraints excluded: chain T residue 197 ASN Chi-restraints excluded: chain T residue 234 TYR Chi-restraints excluded: chain T residue 304 HIS Chi-restraints excluded: chain T residue 319 THR Chi-restraints excluded: chain T residue 362 ILE Chi-restraints excluded: chain T residue 379 THR Chi-restraints excluded: chain T residue 417 ILE Chi-restraints excluded: chain T residue 459 PHE Chi-restraints excluded: chain T residue 460 PHE Chi-restraints excluded: chain T residue 488 THR Chi-restraints excluded: chain T residue 553 HIS Chi-restraints excluded: chain T residue 597 THR Chi-restraints excluded: chain T residue 614 SER Chi-restraints excluded: chain T residue 630 PHE Chi-restraints excluded: chain T residue 695 ASP Chi-restraints excluded: chain T residue 702 PHE Chi-restraints excluded: chain T residue 732 ASP Chi-restraints excluded: chain T residue 767 VAL Chi-restraints excluded: chain T residue 816 SER Chi-restraints excluded: chain T residue 843 ILE Chi-restraints excluded: chain T residue 848 VAL Chi-restraints excluded: chain T residue 913 THR Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 73 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 43 optimal weight: 2.9990 chunk 4 optimal weight: 0.0870 chunk 7 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... T 90 GLN ** T 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 726 GLN ** T 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.145704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.120595 restraints weight = 29805.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.123298 restraints weight = 20092.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.125140 restraints weight = 12988.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.126258 restraints weight = 8237.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.127505 restraints weight = 7191.415| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.191 10144 Z= 0.224 Angle : 0.942 59.189 13663 Z= 0.535 Chirality : 0.044 0.452 1416 Planarity : 0.004 0.079 1788 Dihedral : 6.310 48.394 1375 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.79 % Favored : 86.04 % Rotamer: Outliers : 4.18 % Allowed : 25.64 % Favored : 70.18 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.24), residues: 1227 helix: -0.34 (0.28), residues: 355 sheet: -2.07 (0.27), residues: 359 loop : -2.90 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 910 TYR 0.013 0.001 TYR T 502 PHE 0.014 0.001 PHE T 460 TRP 0.007 0.001 TRP T 287 HIS 0.083 0.003 HIS T 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.22 (10142) covalent geometry : angle 0.94215 / 0.53 (13659) SS BOND : bond 0.00056 / 0.03 ( 2) SS BOND : angle 0.88997 / 0.32 ( 4) hydrogen bonds : bond 0.03289 / 2.18 ( 372) hydrogen bonds : angle 4.99619 / 3.47 ( 1046) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 163 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 68 ASP cc_start: 0.6461 (OUTLIER) cc_final: 0.6206 (p0) REVERT: T 92 LYS cc_start: 0.8175 (mttm) cc_final: 0.7963 (mttm) REVERT: T 156 PHE cc_start: 0.6139 (t80) cc_final: 0.5820 (t80) REVERT: T 361 LYS cc_start: 0.7758 (ttpt) cc_final: 0.7234 (mttp) REVERT: T 630 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7421 (t80) REVERT: T 707 ASN cc_start: 0.8364 (t0) cc_final: 0.7924 (t0) REVERT: T 732 ASP cc_start: 0.7131 (OUTLIER) cc_final: 0.6748 (p0) REVERT: A 7 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8463 (ttpp) REVERT: B 11 ASN cc_start: 0.7994 (t0) cc_final: 0.7764 (t0) REVERT: D 22 TYR cc_start: 0.8075 (m-80) cc_final: 0.7781 (m-80) REVERT: D 52 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7984 (mp0) REVERT: D 60 GLU cc_start: 0.7669 (tp30) cc_final: 0.7461 (tp30) outliers start: 42 outliers final: 35 residues processed: 191 average time/residue: 0.0957 time to fit residues: 26.3686 Evaluate side-chains 199 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 160 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 56 VAL Chi-restraints excluded: chain T residue 68 ASP Chi-restraints excluded: chain T residue 69 VAL Chi-restraints excluded: chain T residue 90 GLN Chi-restraints excluded: chain T residue 120 THR Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain T residue 165 LEU Chi-restraints excluded: chain T residue 234 TYR Chi-restraints excluded: chain T residue 319 THR Chi-restraints excluded: chain T residue 362 ILE Chi-restraints excluded: chain T residue 379 THR Chi-restraints excluded: chain T residue 417 ILE Chi-restraints excluded: chain T residue 459 PHE Chi-restraints excluded: chain T residue 460 PHE Chi-restraints excluded: chain T residue 488 THR Chi-restraints excluded: chain T residue 553 HIS Chi-restraints excluded: chain T residue 597 THR Chi-restraints excluded: chain T residue 614 SER Chi-restraints excluded: chain T residue 630 PHE Chi-restraints excluded: chain T residue 695 ASP Chi-restraints excluded: chain T residue 702 PHE Chi-restraints excluded: chain T residue 732 ASP Chi-restraints excluded: chain T residue 767 VAL Chi-restraints excluded: chain T residue 816 SER Chi-restraints excluded: chain T residue 843 ILE Chi-restraints excluded: chain T residue 848 VAL Chi-restraints excluded: chain T residue 913 THR Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 49 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 115 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 726 GLN ** T 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 HIS ** 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 = 0.3694 r_free = 0.3694 target = 0.145892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.121212 restraints weight = 32134.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.123285 restraints weight = 22564.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.125439 restraints weight = 14093.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.128336 restraints weight = 8757.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.128924 restraints weight = 7039.459| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.201 10144 Z= 0.268 Angle : 1.126 59.184 13663 Z= 0.659 Chirality : 0.066 1.894 1416 Planarity : 0.004 0.060 1788 Dihedral : 6.301 48.416 1375 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.96 % Favored : 85.88 % Rotamer: Outliers : 3.89 % Allowed : 25.55 % Favored : 70.56 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.24), residues: 1227 helix: -0.34 (0.27), residues: 355 sheet: -2.07 (0.27), residues: 359 loop : -2.91 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 910 TYR 0.013 0.001 TYR T 502 PHE 0.014 0.001 PHE T 460 TRP 0.007 0.001 TRP T 287 HIS 0.059 0.002 HIS T 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.27 (10142) covalent geometry : angle 1.12577 / 0.66 (13659) SS BOND : bond 0.00034 / 0.02 ( 2) SS BOND : angle 0.87822 / 0.32 ( 4) hydrogen bonds : bond 0.03307 / 2.19 ( 372) hydrogen bonds : angle 4.99546 / 3.47 ( 1046) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1747.94 seconds wall clock time: 31 minutes 12.87 seconds (1872.87 seconds total)