Starting phenix.real_space_refine on Wed Feb 4 10:11:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oaa_70277/02_2026/9oaa_70277.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oaa_70277/02_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_70277/02_2026/9oaa_70277.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oaa_70277/02_2026/9oaa_70277.map" model { file = "/net/cci-nas-00/data/ceres_data/9oaa_70277/02_2026/9oaa_70277.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oaa_70277/02_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-2.0-5952/lib/python3.9/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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 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: 2.39, per 1000 atoms: 0.24 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: 0.79 Conformation dependent library (CDL) restraints added in 375.9 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: 0.26 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: 1.34 Time building geometry restraints manager: 1.07 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.660 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 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 covalent geometry : bond 0.00535 (10142) covalent geometry : angle 0.91525 (13659) SS BOND : bond 0.00043 ( 2) SS BOND : angle 0.49488 ( 4) hydrogen bonds : bond 0.23424 ( 372) hydrogen bonds : angle 9.97948 ( 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 : 0.404 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: 0.0985 time to fit residues: 39.6676 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 : 0.395 ------------------------------------------------------------------------------- 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: 0.9980 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: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3682 r_free = 0.3682 target = 0.144355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.119058 restraints weight = 40107.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.123694 restraints weight = 33418.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.128183 restraints weight = 10923.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.130444 restraints weight = 6223.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.131136 restraints weight = 4927.503| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2366 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= 0.205 Angle : 0.705 9.248 13663 Z= 0.371 Chirality : 0.044 0.203 1416 Planarity : 0.005 0.051 1788 Dihedral : 7.226 59.186 1398 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.78 % Favored : 85.06 % Rotamer: Outliers : 4.84 % Allowed : 19.94 % Favored : 75.21 % 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: -3.33 (0.23), residues: 1227 helix: -0.35 (0.28), residues: 345 sheet: -2.56 (0.26), residues: 353 loop : -3.21 (0.24), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 42 TYR 0.023 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 covalent geometry : bond 0.00463 (10142) covalent geometry : angle 0.70449 (13659) SS BOND : bond 0.00077 ( 2) SS BOND : angle 0.76341 ( 4) hydrogen bonds : bond 0.04674 ( 372) hydrogen bonds : angle 5.99652 ( 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: 49 poor density : 206 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 68 ASP cc_start: 0.6289 (OUTLIER) cc_final: 0.6070 (p0) REVERT: T 79 ILE cc_start: 0.8776 (mm) cc_final: 0.8543 (tt) REVERT: T 92 LYS cc_start: 0.8150 (mttm) cc_final: 0.7924 (mttm) REVERT: T 162 ILE cc_start: 0.8866 (tt) cc_final: 0.8647 (tt) REVERT: T 165 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7216 (mp) REVERT: T 304 HIS cc_start: 0.9178 (OUTLIER) cc_final: 0.8726 (t-90) REVERT: T 361 LYS cc_start: 0.7802 (ttpt) cc_final: 0.7387 (mttp) REVERT: T 477 LYS cc_start: 0.8486 (tptp) cc_final: 0.8235 (tptp) REVERT: T 480 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6371 (mttp) REVERT: B 51 LYS cc_start: 0.8799 (ttmm) cc_final: 0.8390 (mtpp) REVERT: B 81 MET cc_start: 0.8701 (tpp) cc_final: 0.8010 (mpp) REVERT: B 83 MET cc_start: 0.7719 (tpp) cc_final: 0.7389 (mmt) REVERT: B 90 SER cc_start: 0.9163 (m) cc_final: 0.8518 (t) REVERT: C 7 LYS cc_start: 0.8746 (mtmt) cc_final: 0.8539 (mttm) REVERT: C 63 ASP cc_start: 0.8043 (p0) cc_final: 0.7802 (p0) REVERT: D 94 MET cc_start: 0.6843 (mmm) cc_final: 0.6402 (mmm) outliers start: 49 outliers final: 28 residues processed: 245 average time/residue: 0.0993 time to fit residues: 34.0182 Evaluate side-chains 212 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 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 480 LYS 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 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 C residue 72 LEU Chi-restraints excluded: chain C residue 75 VAL 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: 1.9990 chunk 106 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 202 ASN T 413 ASN T 602 ASN T 626 ASN T 690 HIS 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.136358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.110034 restraints weight = 34873.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.115699 restraints weight = 26896.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.118784 restraints weight = 9729.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.118983 restraints weight = 6999.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.119845 restraints weight = 6323.940| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 10144 Z= 0.306 Angle : 0.786 8.037 13663 Z= 0.416 Chirality : 0.047 0.250 1416 Planarity : 0.005 0.057 1788 Dihedral : 7.067 59.762 1376 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 16.01 % Favored : 83.83 % Rotamer: Outliers : 6.27 % Allowed : 19.47 % Favored : 74.26 % 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: -3.47 (0.23), residues: 1227 helix: -0.41 (0.28), residues: 345 sheet: -2.65 (0.26), residues: 352 loop : -3.31 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 42 TYR 0.019 0.002 TYR T 234 PHE 0.019 0.002 PHE B 48 TRP 0.014 0.002 TRP T 287 HIS 0.033 0.002 HIS T 304 Details of bonding type rmsd covalent geometry : bond 0.00697 (10142) covalent geometry : angle 0.78610 (13659) SS BOND : bond 0.02016 ( 2) SS BOND : angle 1.48938 ( 4) hydrogen bonds : bond 0.04795 ( 372) hydrogen bonds : angle 5.79528 ( 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 262 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 198 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 92 LYS cc_start: 0.8145 (mttm) cc_final: 0.7898 (mttm) REVERT: T 177 ASP cc_start: 0.7739 (m-30) cc_final: 0.7474 (m-30) REVERT: T 361 LYS cc_start: 0.7862 (ttpt) cc_final: 0.7409 (mttp) REVERT: T 600 MET cc_start: 0.8908 (mmt) cc_final: 0.8685 (mmt) REVERT: T 732 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.7006 (p0) REVERT: A 16 TYR cc_start: 0.8608 (t80) cc_final: 0.8286 (t80) REVERT: B 81 MET cc_start: 0.8834 (tpp) cc_final: 0.8124 (mpp) REVERT: B 90 SER cc_start: 0.9073 (m) cc_final: 0.8804 (t) REVERT: D 38 LYS cc_start: 0.8832 (ttmm) cc_final: 0.8435 (mtpp) outliers start: 64 outliers final: 46 residues processed: 246 average time/residue: 0.0984 time to fit residues: 34.1453 Evaluate side-chains 227 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 180 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 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 848 VAL Chi-restraints excluded: chain T residue 913 THR Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 75 VAL 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 21 LEU Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 30 SER 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: 3.9990 chunk 3 optimal weight: 0.1980 chunk 67 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.0050 chunk 1 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 304 HIS T 413 ASN T 690 HIS ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.144067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.120555 restraints weight = 41944.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.124646 restraints weight = 35973.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.129374 restraints weight = 11954.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.131570 restraints weight = 6229.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.131842 restraints weight = 4913.126| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3495 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3495 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10144 Z= 0.126 Angle : 0.656 7.555 13663 Z= 0.345 Chirality : 0.042 0.186 1416 Planarity : 0.004 0.051 1788 Dihedral : 6.501 53.268 1376 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.46 % Favored : 86.37 % Rotamer: Outliers : 4.75 % Allowed : 22.60 % Favored : 72.65 % 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: -3.05 (0.23), residues: 1227 helix: -0.13 (0.28), residues: 346 sheet: -2.28 (0.28), residues: 337 loop : -3.14 (0.24), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 42 TYR 0.012 0.001 TYR T 291 PHE 0.026 0.002 PHE D 48 TRP 0.008 0.001 TRP T 678 HIS 0.010 0.001 HIS A 17 Details of bonding type rmsd covalent geometry : bond 0.00281 (10142) covalent geometry : angle 0.65597 (13659) SS BOND : bond 0.00032 ( 2) SS BOND : angle 1.41237 ( 4) hydrogen bonds : bond 0.03509 ( 372) hydrogen bonds : angle 5.24117 ( 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 232 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 184 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 92 LYS cc_start: 0.8110 (mttm) cc_final: 0.7856 (mttm) REVERT: T 361 LYS cc_start: 0.7784 (ttpt) cc_final: 0.7242 (mttp) REVERT: T 732 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6726 (p0) REVERT: A 11 SER cc_start: 0.8925 (OUTLIER) cc_final: 0.8719 (t) REVERT: D 38 LYS cc_start: 0.8786 (ttmm) cc_final: 0.8551 (mtpp) outliers start: 48 outliers final: 28 residues processed: 218 average time/residue: 0.0958 time to fit residues: 29.8268 Evaluate side-chains 196 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 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 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 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 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 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 B residue 72 LYS Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 57 GLU 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: 3.9990 chunk 102 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 304 HIS ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3650 r_free = 0.3650 target = 0.142740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.118072 restraints weight = 44265.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.122578 restraints weight = 35408.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.127198 restraints weight = 11758.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.129426 restraints weight = 6462.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.129817 restraints weight = 4927.931| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3407 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3516 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= 0.176 Angle : 0.675 7.671 13663 Z= 0.353 Chirality : 0.043 0.221 1416 Planarity : 0.004 0.055 1788 Dihedral : 6.556 48.650 1376 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.11 % Favored : 84.73 % Rotamer: Outliers : 5.79 % Allowed : 22.22 % Favored : 71.98 % 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: -3.07 (0.23), residues: 1227 helix: -0.15 (0.28), residues: 352 sheet: -2.25 (0.28), residues: 339 loop : -3.19 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 42 TYR 0.025 0.001 TYR T 387 PHE 0.018 0.002 PHE T 460 TRP 0.010 0.001 TRP T 287 HIS 0.005 0.001 HIS D 91 Details of bonding type rmsd covalent geometry : bond 0.00402 (10142) covalent geometry : angle 0.67427 (13659) SS BOND : bond 0.00076 ( 2) SS BOND : angle 1.31341 ( 4) hydrogen bonds : bond 0.03646 ( 372) hydrogen bonds : angle 5.20499 ( 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 234 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 175 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 92 LYS cc_start: 0.8177 (mttm) cc_final: 0.7918 (mttm) REVERT: T 177 ASP cc_start: 0.7920 (m-30) cc_final: 0.7693 (m-30) REVERT: T 304 HIS cc_start: 0.9193 (OUTLIER) cc_final: 0.8791 (t70) REVERT: T 361 LYS cc_start: 0.7882 (ttpt) cc_final: 0.7304 (mttp) REVERT: T 561 TYR cc_start: 0.7522 (t80) cc_final: 0.7312 (t80) REVERT: T 630 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7627 (t80) REVERT: T 732 ASP cc_start: 0.7260 (OUTLIER) cc_final: 0.6893 (p0) REVERT: B 83 MET cc_start: 0.8021 (mmm) cc_final: 0.7634 (mmm) outliers start: 59 outliers final: 40 residues processed: 217 average time/residue: 0.0843 time to fit residues: 26.3719 Evaluate side-chains 209 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 166 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 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 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 460 PHE 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 663 ASN Chi-restraints excluded: chain T residue 677 SER 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 A residue 75 VAL 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 17 ASN 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: 0.9990 chunk 29 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 113 optimal weight: 0.3980 chunk 119 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 311 ASN ** B 105 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 = 0.3646 r_free = 0.3646 target = 0.142163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.117055 restraints weight = 36878.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.122412 restraints weight = 32574.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.125928 restraints weight = 11189.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.127079 restraints weight = 7376.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.127830 restraints weight = 6060.714| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3401 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 10144 Z= 0.150 Angle : 0.662 7.177 13663 Z= 0.345 Chirality : 0.042 0.185 1416 Planarity : 0.004 0.052 1788 Dihedral : 6.437 46.821 1375 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.20 % Favored : 85.63 % Rotamer: Outliers : 5.13 % Allowed : 23.46 % Favored : 71.42 % 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: -2.98 (0.24), residues: 1227 helix: -0.06 (0.28), residues: 345 sheet: -2.24 (0.28), residues: 355 loop : -3.09 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 31 TYR 0.012 0.001 TYR T 291 PHE 0.014 0.001 PHE T 460 TRP 0.008 0.001 TRP T 678 HIS 0.005 0.001 HIS T 304 Details of bonding type rmsd covalent geometry : bond 0.00347 (10142) covalent geometry : angle 0.66172 (13659) SS BOND : bond 0.00067 ( 2) SS BOND : angle 1.13572 ( 4) hydrogen bonds : bond 0.03473 ( 372) hydrogen bonds : angle 5.15991 ( 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 235 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 183 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 92 LYS cc_start: 0.8187 (mttm) cc_final: 0.7933 (mttm) REVERT: T 156 PHE cc_start: 0.6337 (t80) cc_final: 0.6020 (t80) REVERT: T 177 ASP cc_start: 0.7901 (m-30) cc_final: 0.7678 (m-30) REVERT: T 196 THR cc_start: 0.8132 (m) cc_final: 0.7751 (m) REVERT: T 361 LYS cc_start: 0.7789 (ttpt) cc_final: 0.7282 (mttp) REVERT: T 480 LYS cc_start: 0.6919 (OUTLIER) cc_final: 0.6422 (mttp) REVERT: T 606 MET cc_start: 0.7821 (mtp) cc_final: 0.7496 (mtp) REVERT: T 630 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7549 (t80) REVERT: T 732 ASP cc_start: 0.7211 (OUTLIER) cc_final: 0.6843 (p0) REVERT: B 83 MET cc_start: 0.7989 (mmm) cc_final: 0.7706 (mmm) REVERT: D 13 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6832 (tm-30) outliers start: 52 outliers final: 41 residues processed: 218 average time/residue: 0.0876 time to fit residues: 27.8264 Evaluate side-chains 213 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 169 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 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 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 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 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 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 A residue 75 VAL 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 49 LEU Chi-restraints excluded: chain D residue 73 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 22 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 chunk 80 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 304 HIS T 413 ASN ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 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 = 0.3672 r_free = 0.3672 target = 0.144384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.119492 restraints weight = 28674.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.121812 restraints weight = 20831.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.123954 restraints weight = 13538.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.124979 restraints weight = 8578.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.126318 restraints weight = 7533.246| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 10144 Z= 0.158 Angle : 0.668 9.725 13663 Z= 0.350 Chirality : 0.043 0.206 1416 Planarity : 0.004 0.050 1788 Dihedral : 6.485 50.463 1375 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.45 % Favored : 85.39 % Rotamer: Outliers : 5.32 % Allowed : 24.31 % Favored : 70.37 % 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: -2.96 (0.24), residues: 1227 helix: -0.04 (0.28), residues: 345 sheet: -2.29 (0.27), residues: 361 loop : -3.02 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 109 TYR 0.025 0.001 TYR T 387 PHE 0.016 0.001 PHE T 460 TRP 0.009 0.001 TRP T 287 HIS 0.004 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00363 (10142) covalent geometry : angle 0.66824 (13659) SS BOND : bond 0.00049 ( 2) SS BOND : angle 1.03628 ( 4) hydrogen bonds : bond 0.03523 ( 372) hydrogen bonds : angle 5.07660 ( 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 227 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 173 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 177 ASP cc_start: 0.7809 (m-30) cc_final: 0.7586 (m-30) REVERT: T 190 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8395 (tt) REVERT: T 196 THR cc_start: 0.8067 (m) cc_final: 0.7700 (m) REVERT: T 304 HIS cc_start: 0.9069 (OUTLIER) cc_final: 0.8697 (t70) REVERT: T 361 LYS cc_start: 0.7758 (ttpt) cc_final: 0.7379 (mttp) REVERT: T 421 ASN cc_start: 0.7831 (t0) cc_final: 0.7585 (m-40) REVERT: T 477 LYS cc_start: 0.8534 (tptp) cc_final: 0.8184 (tptp) REVERT: T 480 LYS cc_start: 0.6829 (OUTLIER) cc_final: 0.6475 (mttp) REVERT: T 606 MET cc_start: 0.7823 (mtp) cc_final: 0.7573 (mtp) REVERT: T 630 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7530 (t80) REVERT: T 669 TRP cc_start: 0.8237 (m100) cc_final: 0.7856 (m100) REVERT: T 732 ASP cc_start: 0.7217 (OUTLIER) cc_final: 0.6726 (p0) REVERT: A 7 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8629 (ttpp) REVERT: B 83 MET cc_start: 0.7933 (mmm) cc_final: 0.7651 (mmm) REVERT: C 12 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8282 (tt) REVERT: D 36 GLU cc_start: 0.7045 (pt0) cc_final: 0.6675 (pt0) REVERT: D 52 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8072 (mp0) REVERT: D 60 GLU cc_start: 0.7742 (tp30) cc_final: 0.7452 (tp30) outliers start: 54 outliers final: 40 residues processed: 214 average time/residue: 0.0910 time to fit residues: 28.2943 Evaluate side-chains 211 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 164 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 56 VAL Chi-restraints excluded: chain T residue 69 VAL Chi-restraints excluded: chain T residue 72 SER 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 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 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 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 677 SER 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 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 A residue 75 VAL 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 12 ILE Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 73 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 47 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 90 GLN T 413 ASN ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 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 = 0.3618 r_free = 0.3618 target = 0.139670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.114116 restraints weight = 33346.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.120124 restraints weight = 27790.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.122594 restraints weight = 10141.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.123112 restraints weight = 7428.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.124020 restraints weight = 6677.427| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10144 Z= 0.194 Angle : 0.692 8.433 13663 Z= 0.364 Chirality : 0.044 0.217 1416 Planarity : 0.004 0.050 1788 Dihedral : 6.651 57.994 1375 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.35 % Favored : 84.48 % Rotamer: Outliers : 5.22 % Allowed : 24.22 % 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: -3.03 (0.24), residues: 1227 helix: -0.13 (0.28), residues: 347 sheet: -2.36 (0.27), residues: 365 loop : -3.03 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG T 599 TYR 0.020 0.001 TYR C 16 PHE 0.015 0.002 PHE T 460 TRP 0.009 0.001 TRP T 287 HIS 0.007 0.001 HIS T 304 Details of bonding type rmsd covalent geometry : bond 0.00445 (10142) covalent geometry : angle 0.69227 (13659) SS BOND : bond 0.00059 ( 2) SS BOND : angle 1.07177 ( 4) hydrogen bonds : bond 0.03720 ( 372) hydrogen bonds : angle 5.11728 ( 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 224 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 171 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 92 LYS cc_start: 0.8096 (mttm) cc_final: 0.7760 (mttm) REVERT: T 177 ASP cc_start: 0.7683 (m-30) cc_final: 0.7479 (m-30) REVERT: T 190 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8424 (tt) REVERT: T 196 THR cc_start: 0.8070 (m) cc_final: 0.7764 (m) REVERT: T 304 HIS cc_start: 0.9249 (OUTLIER) cc_final: 0.8178 (t-90) REVERT: T 361 LYS cc_start: 0.7799 (ttpt) cc_final: 0.7308 (mttp) REVERT: T 477 LYS cc_start: 0.8517 (tptp) cc_final: 0.8211 (tptp) REVERT: T 480 LYS cc_start: 0.6745 (OUTLIER) cc_final: 0.6341 (mttp) REVERT: T 606 MET cc_start: 0.7903 (mtp) cc_final: 0.7622 (mtp) REVERT: T 630 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.7646 (t80) REVERT: T 732 ASP cc_start: 0.7208 (OUTLIER) cc_final: 0.6876 (p0) REVERT: A 7 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8494 (ttpp) REVERT: B 83 MET cc_start: 0.7996 (mmm) cc_final: 0.7634 (mmm) REVERT: D 38 LYS cc_start: 0.9006 (mtpt) cc_final: 0.8652 (mtpp) REVERT: D 60 GLU cc_start: 0.7795 (tp30) cc_final: 0.7425 (tp30) outliers start: 53 outliers final: 40 residues processed: 209 average time/residue: 0.0915 time to fit residues: 27.7680 Evaluate side-chains 208 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 162 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 56 VAL Chi-restraints excluded: chain T residue 69 VAL Chi-restraints excluded: chain T residue 72 SER 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 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 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 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 677 SER 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 105 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 90 GLN T 304 HIS T 413 ASN T 726 GLN ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN C 87 ASN D 73 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.143304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.117448 restraints weight = 36687.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.123810 restraints weight = 29250.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.127003 restraints weight = 9825.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.127755 restraints weight = 6833.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.128681 restraints weight = 5877.021| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10144 Z= 0.174 Angle : 0.682 7.679 13663 Z= 0.359 Chirality : 0.044 0.247 1416 Planarity : 0.004 0.058 1788 Dihedral : 6.561 51.666 1375 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.02 % Favored : 84.81 % Rotamer: Outliers : 5.13 % Allowed : 25.07 % Favored : 69.80 % 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: -3.09 (0.23), residues: 1227 helix: -0.39 (0.27), residues: 353 sheet: -2.31 (0.27), residues: 363 loop : -2.99 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG T 599 TYR 0.026 0.001 TYR T 387 PHE 0.014 0.002 PHE T 460 TRP 0.008 0.001 TRP T 678 HIS 0.004 0.001 HIS T 662 Details of bonding type rmsd covalent geometry : bond 0.00399 (10142) covalent geometry : angle 0.68143 (13659) SS BOND : bond 0.00050 ( 2) SS BOND : angle 1.02479 ( 4) hydrogen bonds : bond 0.03679 ( 372) hydrogen bonds : angle 5.10597 ( 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 218 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 166 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 92 LYS cc_start: 0.8166 (mttm) cc_final: 0.7867 (mttm) REVERT: T 177 ASP cc_start: 0.7757 (m-30) cc_final: 0.7546 (m-30) REVERT: T 190 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8346 (tt) REVERT: T 196 THR cc_start: 0.8063 (m) cc_final: 0.7771 (m) REVERT: T 304 HIS cc_start: 0.9155 (OUTLIER) cc_final: 0.8758 (t70) REVERT: T 361 LYS cc_start: 0.7840 (ttpt) cc_final: 0.7260 (mttp) REVERT: T 477 LYS cc_start: 0.8553 (tptp) cc_final: 0.8212 (tptp) REVERT: T 480 LYS cc_start: 0.6842 (OUTLIER) cc_final: 0.6360 (mttp) REVERT: T 606 MET cc_start: 0.7914 (mtp) cc_final: 0.7648 (mtp) REVERT: T 630 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7561 (t80) REVERT: T 732 ASP cc_start: 0.7325 (OUTLIER) cc_final: 0.6943 (p0) REVERT: A 7 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8544 (ttpp) REVERT: B 11 ASN cc_start: 0.8093 (t0) cc_final: 0.7850 (t0) REVERT: B 83 MET cc_start: 0.7945 (mmm) cc_final: 0.7624 (mmm) REVERT: C 16 TYR cc_start: 0.8617 (t80) cc_final: 0.8415 (t80) REVERT: D 36 GLU cc_start: 0.7691 (mp0) cc_final: 0.7451 (pm20) REVERT: D 38 LYS cc_start: 0.9010 (mtpt) cc_final: 0.8734 (mtpp) REVERT: D 60 GLU cc_start: 0.7800 (tp30) cc_final: 0.7577 (tp30) outliers start: 52 outliers final: 39 residues processed: 207 average time/residue: 0.0916 time to fit residues: 27.6783 Evaluate side-chains 208 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 163 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 56 VAL Chi-restraints excluded: chain T residue 69 VAL Chi-restraints excluded: chain T residue 72 SER 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 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 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 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 677 SER 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 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 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 12 ILE 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: 1.9990 chunk 57 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 10 optimal weight: 0.2980 chunk 8 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 304 HIS T 413 ASN T 726 GLN D 73 GLN ** D 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.147162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.122249 restraints weight = 29461.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.124928 restraints weight = 21435.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.126850 restraints weight = 13973.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.128438 restraints weight = 8820.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.129353 restraints weight = 7455.218| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3438 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3438 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3918 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= 0.130 Angle : 0.669 7.284 13663 Z= 0.350 Chirality : 0.043 0.203 1416 Planarity : 0.004 0.060 1788 Dihedral : 6.405 50.359 1375 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.12 % Favored : 85.71 % Rotamer: Outliers : 4.08 % Allowed : 25.93 % Favored : 69.99 % 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: -2.98 (0.24), residues: 1227 helix: -0.38 (0.28), residues: 352 sheet: -2.16 (0.27), residues: 359 loop : -2.92 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 42 TYR 0.014 0.001 TYR C 16 PHE 0.016 0.001 PHE D 79 TRP 0.008 0.001 TRP T 678 HIS 0.010 0.001 HIS T 304 Details of bonding type rmsd covalent geometry : bond 0.00290 (10142) covalent geometry : angle 0.66857 (13659) SS BOND : bond 0.00065 ( 2) SS BOND : angle 0.92498 ( 4) hydrogen bonds : bond 0.03491 ( 372) hydrogen bonds : angle 5.00852 ( 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 216 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 175 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 92 LYS cc_start: 0.8100 (mttm) cc_final: 0.7766 (mttm) REVERT: T 156 PHE cc_start: 0.6073 (t80) cc_final: 0.5746 (t80) REVERT: T 177 ASP cc_start: 0.7746 (m-30) cc_final: 0.7542 (m-30) REVERT: T 304 HIS cc_start: 0.8999 (OUTLIER) cc_final: 0.8752 (t70) REVERT: T 361 LYS cc_start: 0.7776 (ttpt) cc_final: 0.7250 (mttp) REVERT: T 421 ASN cc_start: 0.7877 (t0) cc_final: 0.7668 (m-40) REVERT: T 477 LYS cc_start: 0.8462 (tptp) cc_final: 0.8140 (tptp) REVERT: T 480 LYS cc_start: 0.6740 (OUTLIER) cc_final: 0.6286 (mttp) REVERT: T 606 MET cc_start: 0.7806 (mtp) cc_final: 0.7562 (mtp) REVERT: T 630 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.7443 (t80) REVERT: T 669 TRP cc_start: 0.8125 (m100) cc_final: 0.7614 (m100) REVERT: T 732 ASP cc_start: 0.7161 (OUTLIER) cc_final: 0.6730 (p0) REVERT: A 7 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8492 (ttpp) REVERT: B 83 MET cc_start: 0.7906 (mmm) cc_final: 0.7653 (mmm) REVERT: D 38 LYS cc_start: 0.8984 (mtpt) cc_final: 0.8774 (mtpp) REVERT: D 52 GLU cc_start: 0.8311 (mm-30) cc_final: 0.8002 (mp0) REVERT: D 60 GLU cc_start: 0.7720 (tp30) cc_final: 0.7439 (tp30) outliers start: 41 outliers final: 30 residues processed: 205 average time/residue: 0.0946 time to fit residues: 27.7923 Evaluate side-chains 200 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 56 VAL 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 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 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 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 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 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 12 ILE Chi-restraints excluded: chain C residue 21 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 115 optimal weight: 0.0770 chunk 54 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 413 ASN T 726 GLN ** B 105 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 = 0.3664 r_free = 0.3664 target = 0.143826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.118847 restraints weight = 32015.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.122030 restraints weight = 22319.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.123811 restraints weight = 13798.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.125334 restraints weight = 8918.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.126159 restraints weight = 7499.605| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3318 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3318 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10144 Z= 0.178 Angle : 0.690 8.029 13663 Z= 0.365 Chirality : 0.044 0.205 1416 Planarity : 0.004 0.058 1788 Dihedral : 6.492 50.564 1375 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.86 % Favored : 84.98 % Rotamer: Outliers : 3.51 % Allowed : 26.69 % Favored : 69.80 % 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: -3.02 (0.24), residues: 1227 helix: -0.36 (0.28), residues: 351 sheet: -2.22 (0.27), residues: 356 loop : -2.97 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 910 TYR 0.027 0.001 TYR T 387 PHE 0.017 0.002 PHE D 79 TRP 0.018 0.001 TRP T 287 HIS 0.005 0.001 HIS T 304 Details of bonding type rmsd covalent geometry : bond 0.00408 (10142) covalent geometry : angle 0.68964 (13659) SS BOND : bond 0.00039 ( 2) SS BOND : angle 0.98405 ( 4) hydrogen bonds : bond 0.03668 ( 372) hydrogen bonds : angle 5.05784 ( 1046) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1607.94 seconds wall clock time: 28 minutes 45.54 seconds (1725.54 seconds total)