Starting phenix.real_space_refine on Wed Mar 4 17:56:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x1m_32944/03_2026/7x1m_32944.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x1m_32944/03_2026/7x1m_32944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7x1m_32944/03_2026/7x1m_32944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x1m_32944/03_2026/7x1m_32944.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x1m_32944/03_2026/7x1m_32944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x1m_32944/03_2026/7x1m_32944.map" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.079 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6609 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 6249 2.51 5 N 1657 2.21 5 O 1965 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9908 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1701 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 212} Chain breaks: 1 Chain: "B" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1615 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 200} Chain: "C" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1615 Classifications: {'peptide': 219} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} Chain: "D" Number of atoms: 1637 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 213, 1632 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Conformer: "B" Number of residues, atoms: 213, 1632 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} bond proxies already assigned to first conformer: 1659 Chain: "H" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 921 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "M" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1565 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.63, per 1000 atoms: 0.27 Number of scatterers: 9908 At special positions: 0 Unit cell: (85, 110.5, 169.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1965 8.00 N 1657 7.00 C 6249 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 210 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.04 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 144 " - pdb=" SG CYS C 200 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.05 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS M 336 " - pdb=" SG CYS M 361 " distance=2.03 Simple disulfide: pdb=" SG CYS M 379 " - pdb=" SG CYS M 432 " distance=2.04 Simple disulfide: pdb=" SG CYS M 391 " - pdb=" SG CYS M 525 " distance=2.03 Simple disulfide: pdb=" SG CYS M 480 " - pdb=" SG CYS M 488 " 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " BETA1-6 " NAG E 1 " - " FUC E 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG E 1 " - " ASN M 343 " Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 559.9 milliseconds 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 32 sheets defined 8.7% alpha, 42.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.618A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.845A pdb=" N ASP A 90 " --> pdb=" O ARG A 87 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 91' Processing helix chain 'A' and resid 215 through 218 Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.534A pdb=" N PHE B 84 " --> pdb=" O PRO B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 3.734A pdb=" N LYS B 126 " --> pdb=" O ASP B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 189 Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.880A pdb=" N ASN C 32 " --> pdb=" O VAL C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.799A pdb=" N THR C 90 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'D' and resid 121 through 128 removed outlier: 3.881A pdb=" N LEU D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 187 removed outlier: 3.599A pdb=" N GLU D 187 " --> pdb=" O LYS D 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 183 through 187' Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.587A pdb=" N ASP H 89 " --> pdb=" O ARG H 86 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 86 through 90' Processing helix chain 'M' and resid 338 through 343 removed outlier: 3.631A pdb=" N PHE M 342 " --> pdb=" O PHE M 338 " (cutoff:3.500A) Processing helix chain 'M' and resid 349 through 353 removed outlier: 3.665A pdb=" N TRP M 353 " --> pdb=" O VAL M 350 " (cutoff:3.500A) Processing helix chain 'M' and resid 365 through 370 Processing helix chain 'M' and resid 383 through 387 removed outlier: 3.561A pdb=" N LEU M 387 " --> pdb=" O PRO M 384 " (cutoff:3.500A) Processing helix chain 'M' and resid 403 through 410 removed outlier: 3.891A pdb=" N VAL M 407 " --> pdb=" O GLY M 404 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ARG M 408 " --> pdb=" O ASP M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 422 Processing helix chain 'M' and resid 438 through 443 removed outlier: 3.534A pdb=" N SER M 443 " --> pdb=" O ASN M 439 " (cutoff:3.500A) Processing helix chain 'M' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60 removed outlier: 5.379A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY A 33 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASN A 116 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60 removed outlier: 5.379A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY A 33 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 92 " --> pdb=" O VAL A 123 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 136 through 138 removed outlier: 6.362A pdb=" N TYR A 190 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 136 through 138 removed outlier: 6.362A pdb=" N TYR A 190 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 165 through 168 Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'B' and resid 12 through 13 Processing sheet with id=AA9, first strand: chain 'B' and resid 54 through 55 removed outlier: 6.639A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYR B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 54 through 55 removed outlier: 6.639A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYR B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 130 through 139 removed outlier: 3.593A pdb=" N ALA B 130 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 181 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN B 138 " --> pdb=" O TYR B 173 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR B 173 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AB4, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.996A pdb=" N TYR C 33 " --> pdb=" O ASP C 98 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N MET C 34 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA C 40 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 11 through 12 removed outlier: 4.074A pdb=" N VAL C 106 " --> pdb=" O ARG C 97 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 126 through 128 removed outlier: 3.537A pdb=" N LEU C 142 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER C 184 " --> pdb=" O CYS C 144 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 126 through 128 removed outlier: 5.169A pdb=" N LYS C 147 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU C 182 " --> pdb=" O LYS C 147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 154 through 158 removed outlier: 3.513A pdb=" N SER C 157 " --> pdb=" O ASN C 201 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N TYR C 198 " --> pdb=" O VAL C 215 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.575A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 114 through 118 removed outlier: 3.769A pdb=" N GLN D 160 " --> pdb=" O THR D 178 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.564A pdb=" N CYS D 194 " --> pdb=" O LYS D 207 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS D 207 " --> pdb=" O CYS D 194 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL D 196 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL D 205 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AC7, first strand: chain 'H' and resid 57 through 58 removed outlier: 3.654A pdb=" N THR H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N THR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N MET H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASP H 33 " --> pdb=" O GLY H 98 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY H 98 " --> pdb=" O ASP H 33 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N CYS H 95 " --> pdb=" O TRP H 110 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N TRP H 110 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ARG H 97 " --> pdb=" O ASP H 108 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR H 104 " --> pdb=" O SER H 101 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 57 through 58 removed outlier: 3.654A pdb=" N THR H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N THR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N MET H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASP H 33 " --> pdb=" O GLY H 98 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY H 98 " --> pdb=" O ASP H 33 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.775A pdb=" N ALA L 84 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.775A pdb=" N ALA L 84 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR L 98 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 93 through 94 removed outlier: 3.743A pdb=" N ASN M 394 " --> pdb=" O GLU M 516 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 452 through 454 Processing sheet with id=AD5, first strand: chain 'M' and resid 473 through 474 409 hydrogen bonds defined for protein. 1008 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: 1.75 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2195 1.33 - 1.46: 3389 1.46 - 1.59: 4512 1.59 - 1.72: 0 1.72 - 1.85: 46 Bond restraints: 10142 Sorted by residual: bond pdb=" C ASP H 33 " pdb=" O ASP H 33 " ideal model delta sigma weight residual 1.234 1.198 0.036 1.40e-02 5.10e+03 6.62e+00 bond pdb=" N LYS H 64 " pdb=" CA LYS H 64 " ideal model delta sigma weight residual 1.457 1.487 -0.031 1.31e-02 5.83e+03 5.51e+00 bond pdb=" C ASP H 33 " pdb=" N MET H 34 " ideal model delta sigma weight residual 1.331 1.301 0.030 1.33e-02 5.65e+03 5.21e+00 bond pdb=" CA ASP H 33 " pdb=" C ASP H 33 " ideal model delta sigma weight residual 1.528 1.500 0.028 1.38e-02 5.25e+03 4.16e+00 bond pdb=" C LYS A 215 " pdb=" N PRO A 216 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.08e-02 8.57e+03 3.88e+00 ... (remaining 10137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 13429 2.36 - 4.72: 328 4.72 - 7.08: 31 7.08 - 9.44: 4 9.44 - 11.80: 2 Bond angle restraints: 13794 Sorted by residual: angle pdb=" N ASP H 33 " pdb=" CA ASP H 33 " pdb=" C ASP H 33 " ideal model delta sigma weight residual 110.41 103.26 7.15 1.23e+00 6.61e-01 3.38e+01 angle pdb=" N TYR M 495 " pdb=" CA TYR M 495 " pdb=" C TYR M 495 " ideal model delta sigma weight residual 111.07 116.46 -5.39 1.07e+00 8.73e-01 2.53e+01 angle pdb=" N GLY C 44 " pdb=" CA GLY C 44 " pdb=" C GLY C 44 " ideal model delta sigma weight residual 112.08 116.25 -4.17 1.01e+00 9.80e-01 1.70e+01 angle pdb=" C VAL D 150 " pdb=" N ASP D 151 " pdb=" CA ASP D 151 " ideal model delta sigma weight residual 121.54 129.27 -7.73 1.91e+00 2.74e-01 1.64e+01 angle pdb=" C SER M 494 " pdb=" N TYR M 495 " pdb=" CA TYR M 495 " ideal model delta sigma weight residual 120.44 125.46 -5.02 1.30e+00 5.92e-01 1.49e+01 ... (remaining 13789 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 5560 17.08 - 34.16: 409 34.16 - 51.24: 70 51.24 - 68.32: 12 68.32 - 85.40: 14 Dihedral angle restraints: 6065 sinusoidal: 2345 harmonic: 3720 Sorted by residual: dihedral pdb=" CA GLU A 162 " pdb=" C GLU A 162 " pdb=" N PRO A 163 " pdb=" CA PRO A 163 " ideal model delta harmonic sigma weight residual -180.00 -123.95 -56.05 0 5.00e+00 4.00e-02 1.26e+02 dihedral pdb=" CA TYR D 140 " pdb=" C TYR D 140 " pdb=" N PRO D 141 " pdb=" CA PRO D 141 " ideal model delta harmonic sigma weight residual 0.00 32.00 -32.00 0 5.00e+00 4.00e-02 4.10e+01 dihedral pdb=" CA ASN B 152 " pdb=" C ASN B 152 " pdb=" N ALA B 153 " pdb=" CA ALA B 153 " ideal model delta harmonic sigma weight residual -180.00 -150.57 -29.43 0 5.00e+00 4.00e-02 3.46e+01 ... (remaining 6062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1041 0.041 - 0.081: 362 0.081 - 0.122: 116 0.122 - 0.162: 21 0.162 - 0.203: 5 Chirality restraints: 1545 Sorted by residual: chirality pdb=" CA PRO D 141 " pdb=" N PRO D 141 " pdb=" C PRO D 141 " pdb=" CB PRO D 141 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA PRO A 163 " pdb=" N PRO A 163 " pdb=" C PRO A 163 " pdb=" CB PRO A 163 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB THR H 28 " pdb=" CA THR H 28 " pdb=" OG1 THR H 28 " pdb=" CG2 THR H 28 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.05e-01 ... (remaining 1542 not shown) Planarity restraints: 1766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 162 " -0.074 5.00e-02 4.00e+02 1.13e-01 2.06e+01 pdb=" N PRO A 163 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 112 " 0.047 5.00e-02 4.00e+02 7.23e-02 8.36e+00 pdb=" N PRO D 113 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO D 113 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 113 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 140 " 0.041 5.00e-02 4.00e+02 6.26e-02 6.28e+00 pdb=" N PRO D 141 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 141 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 141 " 0.033 5.00e-02 4.00e+02 ... (remaining 1763 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 740 2.74 - 3.28: 9048 3.28 - 3.82: 15202 3.82 - 4.36: 18990 4.36 - 4.90: 33934 Nonbonded interactions: 77914 Sorted by model distance: nonbonded pdb=" OG1 THR H 90 " pdb=" O LEU H 116 " model vdw 2.195 3.040 nonbonded pdb=" O TYR D 192 " pdb=" OG SER D 208 " model vdw 2.220 3.040 nonbonded pdb=" NH1 ARG B 108 " pdb=" O ASP B 170 " model vdw 2.228 3.120 nonbonded pdb=" OG1 THR A 205 " pdb=" OE1 GLN A 206 " model vdw 2.246 3.040 nonbonded pdb=" O SER C 192 " pdb=" OH TYR C 198 " model vdw 2.263 3.040 ... (remaining 77909 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.370 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 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 0.062 10159 Z= 0.243 Angle : 0.881 11.798 13831 Z= 0.515 Chirality : 0.047 0.203 1545 Planarity : 0.007 0.113 1765 Dihedral : 12.808 85.402 3659 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.69 % Favored : 92.08 % Rotamer: Outliers : 0.18 % Allowed : 0.18 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % 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: -1.86 (0.23), residues: 1276 helix: -3.28 (0.48), residues: 61 sheet: -0.57 (0.22), residues: 543 loop : -1.58 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 24 TYR 0.025 0.002 TYR M 495 PHE 0.018 0.002 PHE H 67 TRP 0.008 0.002 TRP A 47 HIS 0.006 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00516 (10142) covalent geometry : angle 0.87681 (13794) SS BOND : bond 0.00894 ( 14) SS BOND : angle 1.92039 ( 28) hydrogen bonds : bond 0.18575 ( 345) hydrogen bonds : angle 8.41261 ( 1008) link_BETA1-4 : bond 0.00047 ( 1) link_BETA1-4 : angle 2.19115 ( 3) link_BETA1-6 : bond 0.00527 ( 1) link_BETA1-6 : angle 2.41967 ( 3) link_NAG-ASN : bond 0.00275 ( 1) link_NAG-ASN : angle 1.05012 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 0.388 Fit side-chains REVERT: B 145 LYS cc_start: 0.7987 (tmmt) cc_final: 0.7774 (ttpt) REVERT: B 169 LYS cc_start: 0.7414 (ttpt) cc_final: 0.6864 (mmmt) REVERT: B 188 LYS cc_start: 0.7181 (ttpt) cc_final: 0.6804 (ttmt) REVERT: B 190 LYS cc_start: 0.6283 (tptt) cc_final: 0.6062 (tptp) REVERT: C 203 ASN cc_start: 0.7070 (t0) cc_final: 0.6834 (t0) outliers start: 1 outliers final: 1 residues processed: 180 average time/residue: 0.6757 time to fit residues: 128.9595 Evaluate side-chains 135 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 389 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.0470 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A 214 HIS B 90 GLN C 201 ASN ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 ASN L 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.161244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.120342 restraints weight = 24046.868| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.91 r_work: 0.3386 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10159 Z= 0.129 Angle : 0.645 9.964 13831 Z= 0.335 Chirality : 0.045 0.211 1545 Planarity : 0.006 0.109 1765 Dihedral : 5.716 55.180 1465 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.96 % Favored : 93.88 % Rotamer: Outliers : 2.09 % Allowed : 8.91 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % 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: -1.45 (0.23), residues: 1276 helix: -2.94 (0.57), residues: 48 sheet: -0.31 (0.23), residues: 534 loop : -1.33 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 61 TYR 0.018 0.001 TYR D 140 PHE 0.013 0.001 PHE M 374 TRP 0.009 0.001 TRP A 47 HIS 0.005 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00291 (10142) covalent geometry : angle 0.64232 (13794) SS BOND : bond 0.00629 ( 14) SS BOND : angle 1.29445 ( 28) hydrogen bonds : bond 0.03923 ( 345) hydrogen bonds : angle 6.32974 ( 1008) link_BETA1-4 : bond 0.00228 ( 1) link_BETA1-4 : angle 1.42971 ( 3) link_BETA1-6 : bond 0.00276 ( 1) link_BETA1-6 : angle 1.80922 ( 3) link_NAG-ASN : bond 0.00445 ( 1) link_NAG-ASN : angle 0.63633 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.372 Fit side-chains REVERT: A 119 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8125 (pt0) REVERT: B 169 LYS cc_start: 0.7385 (ttpt) cc_final: 0.6596 (mmmt) REVERT: B 183 LYS cc_start: 0.6954 (ptpt) cc_final: 0.6748 (ptpp) REVERT: B 188 LYS cc_start: 0.6972 (ttpt) cc_final: 0.6640 (ttmt) REVERT: C 109 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8110 (mp10) REVERT: D 27 GLN cc_start: 0.7420 (OUTLIER) cc_final: 0.7211 (tt0) REVERT: M 339 ASP cc_start: 0.8813 (m-30) cc_final: 0.8519 (m-30) outliers start: 22 outliers final: 14 residues processed: 171 average time/residue: 0.6000 time to fit residues: 109.2479 Evaluate side-chains 155 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 389 ASP Chi-restraints excluded: chain M residue 445 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 56 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 108 optimal weight: 0.5980 chunk 102 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN C 73 ASN C 201 ASN C 204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.159771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.120499 restraints weight = 14545.070| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.27 r_work: 0.3398 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10159 Z= 0.160 Angle : 0.651 8.142 13831 Z= 0.338 Chirality : 0.046 0.213 1545 Planarity : 0.006 0.107 1765 Dihedral : 5.662 54.823 1465 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.14 % Favored : 92.71 % Rotamer: Outliers : 3.36 % Allowed : 11.09 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -1.38 (0.23), residues: 1276 helix: -3.01 (0.56), residues: 48 sheet: -0.24 (0.23), residues: 543 loop : -1.30 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 61 TYR 0.021 0.002 TYR D 140 PHE 0.015 0.002 PHE M 377 TRP 0.007 0.001 TRP A 47 HIS 0.004 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00379 (10142) covalent geometry : angle 0.64676 (13794) SS BOND : bond 0.00773 ( 14) SS BOND : angle 1.51882 ( 28) hydrogen bonds : bond 0.03784 ( 345) hydrogen bonds : angle 6.03455 ( 1008) link_BETA1-4 : bond 0.00099 ( 1) link_BETA1-4 : angle 1.57753 ( 3) link_BETA1-6 : bond 0.00284 ( 1) link_BETA1-6 : angle 1.69162 ( 3) link_NAG-ASN : bond 0.00167 ( 1) link_NAG-ASN : angle 1.04748 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 0.369 Fit side-chains REVERT: A 119 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8073 (pt0) REVERT: A 156 VAL cc_start: 0.8414 (t) cc_final: 0.8189 (m) REVERT: B 145 LYS cc_start: 0.7581 (ttpt) cc_final: 0.7295 (ttpt) REVERT: B 169 LYS cc_start: 0.7409 (ttpt) cc_final: 0.6660 (mmmt) REVERT: B 183 LYS cc_start: 0.6832 (ptpt) cc_final: 0.6575 (ptpp) REVERT: B 188 LYS cc_start: 0.7008 (ttpt) cc_final: 0.6728 (ttmt) REVERT: B 195 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7390 (tm-30) REVERT: C 109 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8070 (mp10) REVERT: H 19 ARG cc_start: 0.7850 (ttt-90) cc_final: 0.7647 (tmt90) REVERT: M 339 ASP cc_start: 0.8742 (m-30) cc_final: 0.8312 (m-30) outliers start: 36 outliers final: 22 residues processed: 164 average time/residue: 0.5872 time to fit residues: 102.7576 Evaluate side-chains 162 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 389 ASP Chi-restraints excluded: chain M residue 445 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN A 211 ASN L 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.158344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.118940 restraints weight = 14735.754| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.27 r_work: 0.3377 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10159 Z= 0.203 Angle : 0.681 9.005 13831 Z= 0.353 Chirality : 0.047 0.218 1545 Planarity : 0.006 0.107 1765 Dihedral : 5.780 54.681 1465 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.37 % Favored : 92.47 % Rotamer: Outliers : 3.91 % Allowed : 12.55 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 1.52 % 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: -1.42 (0.23), residues: 1276 helix: -3.19 (0.51), residues: 54 sheet: -0.14 (0.23), residues: 546 loop : -1.43 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 61 TYR 0.018 0.002 TYR C 33 PHE 0.022 0.002 PHE M 377 TRP 0.010 0.001 TRP A 47 HIS 0.005 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00487 (10142) covalent geometry : angle 0.67661 (13794) SS BOND : bond 0.00870 ( 14) SS BOND : angle 1.68896 ( 28) hydrogen bonds : bond 0.03885 ( 345) hydrogen bonds : angle 6.01712 ( 1008) link_BETA1-4 : bond 0.00020 ( 1) link_BETA1-4 : angle 1.65256 ( 3) link_BETA1-6 : bond 0.00348 ( 1) link_BETA1-6 : angle 1.80277 ( 3) link_NAG-ASN : bond 0.00134 ( 1) link_NAG-ASN : angle 1.31318 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 0.323 Fit side-chains REVERT: A 119 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8100 (pt0) REVERT: A 156 VAL cc_start: 0.8369 (t) cc_final: 0.8097 (m) REVERT: B 145 LYS cc_start: 0.7614 (ttpt) cc_final: 0.7366 (ttpt) REVERT: B 169 LYS cc_start: 0.7385 (ttpt) cc_final: 0.6636 (mmmt) REVERT: B 183 LYS cc_start: 0.6612 (OUTLIER) cc_final: 0.6398 (ptpp) REVERT: B 188 LYS cc_start: 0.6974 (ttpt) cc_final: 0.6668 (ttmt) REVERT: C 109 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8163 (mp10) REVERT: D 185 ASP cc_start: 0.5892 (t0) cc_final: 0.5643 (t0) REVERT: L 83 PHE cc_start: 0.7885 (t80) cc_final: 0.7521 (t80) REVERT: M 339 ASP cc_start: 0.8759 (m-30) cc_final: 0.8478 (m-30) outliers start: 42 outliers final: 25 residues processed: 172 average time/residue: 0.5720 time to fit residues: 105.2934 Evaluate side-chains 154 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 389 ASP Chi-restraints excluded: chain M residue 445 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 50 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 39 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN C 201 ASN D 199 GLN L 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.158311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.118864 restraints weight = 14892.444| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.29 r_work: 0.3375 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10159 Z= 0.188 Angle : 0.672 8.093 13831 Z= 0.348 Chirality : 0.046 0.208 1545 Planarity : 0.006 0.104 1765 Dihedral : 5.730 54.658 1465 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.22 % Favored : 92.63 % Rotamer: Outliers : 4.36 % Allowed : 13.73 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -1.41 (0.23), residues: 1276 helix: -3.38 (0.49), residues: 54 sheet: -0.11 (0.23), residues: 538 loop : -1.42 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 61 TYR 0.016 0.002 TYR C 33 PHE 0.023 0.002 PHE M 377 TRP 0.011 0.001 TRP A 47 HIS 0.005 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00449 (10142) covalent geometry : angle 0.66755 (13794) SS BOND : bond 0.00819 ( 14) SS BOND : angle 1.63489 ( 28) hydrogen bonds : bond 0.03739 ( 345) hydrogen bonds : angle 5.96104 ( 1008) link_BETA1-4 : bond 0.00040 ( 1) link_BETA1-4 : angle 1.68745 ( 3) link_BETA1-6 : bond 0.00302 ( 1) link_BETA1-6 : angle 1.75269 ( 3) link_NAG-ASN : bond 0.00218 ( 1) link_NAG-ASN : angle 1.49510 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 137 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 119 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8166 (pt0) REVERT: A 156 VAL cc_start: 0.8352 (t) cc_final: 0.8081 (m) REVERT: B 126 LYS cc_start: 0.7856 (mmtt) cc_final: 0.7591 (pttp) REVERT: B 145 LYS cc_start: 0.7613 (ttpt) cc_final: 0.7348 (ttpt) REVERT: B 169 LYS cc_start: 0.7382 (ttpt) cc_final: 0.6645 (mmmt) REVERT: B 188 LYS cc_start: 0.7004 (ttpt) cc_final: 0.6679 (ttmt) REVERT: C 109 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8166 (mp10) REVERT: D 140 TYR cc_start: 0.7527 (t80) cc_final: 0.6982 (t80) REVERT: H 19 ARG cc_start: 0.7899 (ttt-90) cc_final: 0.7666 (tmt90) REVERT: H 115 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8715 (tt) REVERT: L 83 PHE cc_start: 0.7908 (t80) cc_final: 0.7549 (t80) outliers start: 47 outliers final: 27 residues processed: 165 average time/residue: 0.5303 time to fit residues: 94.2397 Evaluate side-chains 151 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 389 ASP Chi-restraints excluded: chain M residue 445 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 98 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN C 73 ASN L 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.158441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.118249 restraints weight = 17530.057| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.48 r_work: 0.3365 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10159 Z= 0.188 Angle : 0.676 8.796 13831 Z= 0.348 Chirality : 0.047 0.226 1545 Planarity : 0.006 0.104 1765 Dihedral : 5.700 54.400 1465 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.22 % Favored : 92.63 % Rotamer: Outliers : 3.91 % Allowed : 14.55 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 1.52 % 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: -1.42 (0.23), residues: 1276 helix: -3.43 (0.49), residues: 54 sheet: -0.08 (0.23), residues: 543 loop : -1.45 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 211 TYR 0.016 0.002 TYR D 140 PHE 0.020 0.002 PHE M 377 TRP 0.010 0.001 TRP A 47 HIS 0.005 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00449 (10142) covalent geometry : angle 0.67049 (13794) SS BOND : bond 0.00831 ( 14) SS BOND : angle 1.87438 ( 28) hydrogen bonds : bond 0.03721 ( 345) hydrogen bonds : angle 5.93094 ( 1008) link_BETA1-4 : bond 0.00000 ( 1) link_BETA1-4 : angle 1.67918 ( 3) link_BETA1-6 : bond 0.00274 ( 1) link_BETA1-6 : angle 1.75501 ( 3) link_NAG-ASN : bond 0.00254 ( 1) link_NAG-ASN : angle 1.54081 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 137 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 119 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8199 (pt0) REVERT: B 126 LYS cc_start: 0.7826 (mmtt) cc_final: 0.7573 (pttp) REVERT: B 145 LYS cc_start: 0.7631 (ttpt) cc_final: 0.7330 (ttpt) REVERT: B 169 LYS cc_start: 0.7378 (ttpt) cc_final: 0.6638 (mmmt) REVERT: B 188 LYS cc_start: 0.6938 (ttpt) cc_final: 0.6662 (ttmt) REVERT: C 109 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8154 (mp10) REVERT: H 19 ARG cc_start: 0.7885 (ttt-90) cc_final: 0.7640 (tmt90) REVERT: L 83 PHE cc_start: 0.7929 (t80) cc_final: 0.7561 (t80) outliers start: 42 outliers final: 33 residues processed: 162 average time/residue: 0.5344 time to fit residues: 93.0827 Evaluate side-chains 155 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 376 THR Chi-restraints excluded: chain M residue 389 ASP Chi-restraints excluded: chain M residue 445 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 6 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 121 optimal weight: 0.0030 chunk 67 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN L 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.156853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.116735 restraints weight = 17468.667| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.47 r_work: 0.3345 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 10159 Z= 0.240 Angle : 0.725 7.578 13831 Z= 0.374 Chirality : 0.048 0.212 1545 Planarity : 0.007 0.105 1765 Dihedral : 5.936 54.751 1465 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.84 % Favored : 92.00 % Rotamer: Outliers : 4.73 % Allowed : 14.91 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 1.52 % 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: -1.53 (0.23), residues: 1276 helix: -3.53 (0.46), residues: 54 sheet: -0.15 (0.23), residues: 551 loop : -1.55 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 61 TYR 0.019 0.002 TYR C 33 PHE 0.024 0.002 PHE M 377 TRP 0.011 0.002 TRP A 47 HIS 0.006 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00577 (10142) covalent geometry : angle 0.71833 (13794) SS BOND : bond 0.00969 ( 14) SS BOND : angle 2.04628 ( 28) hydrogen bonds : bond 0.04044 ( 345) hydrogen bonds : angle 6.07393 ( 1008) link_BETA1-4 : bond 0.00071 ( 1) link_BETA1-4 : angle 1.66265 ( 3) link_BETA1-6 : bond 0.00340 ( 1) link_BETA1-6 : angle 1.79587 ( 3) link_NAG-ASN : bond 0.00208 ( 1) link_NAG-ASN : angle 1.74534 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 137 time to evaluate : 0.311 Fit side-chains REVERT: A 119 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8194 (pt0) REVERT: B 126 LYS cc_start: 0.7836 (mmtt) cc_final: 0.7578 (pttp) REVERT: B 143 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7659 (mp0) REVERT: B 145 LYS cc_start: 0.7648 (ttpt) cc_final: 0.7360 (ttpt) REVERT: B 169 LYS cc_start: 0.7412 (ttpt) cc_final: 0.6668 (mmmt) REVERT: B 188 LYS cc_start: 0.6928 (ttpt) cc_final: 0.6704 (ttmt) REVERT: C 109 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8223 (mp10) REVERT: D 27 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.7253 (tt0) REVERT: H 19 ARG cc_start: 0.7898 (ttt-90) cc_final: 0.7641 (tmt90) REVERT: H 115 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8782 (tt) REVERT: L 106 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7920 (m-30) REVERT: M 339 ASP cc_start: 0.8773 (m-30) cc_final: 0.8512 (m-30) outliers start: 51 outliers final: 38 residues processed: 167 average time/residue: 0.5409 time to fit residues: 96.8719 Evaluate side-chains 172 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 106 ASP Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 376 THR Chi-restraints excluded: chain M residue 389 ASP Chi-restraints excluded: chain M residue 445 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 32 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN L 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.157785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.118265 restraints weight = 15372.517| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.31 r_work: 0.3371 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10159 Z= 0.201 Angle : 0.691 7.497 13831 Z= 0.357 Chirality : 0.047 0.209 1545 Planarity : 0.007 0.102 1765 Dihedral : 5.845 54.697 1465 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.14 % Favored : 92.71 % Rotamer: Outliers : 4.09 % Allowed : 15.55 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -1.52 (0.23), residues: 1276 helix: -3.59 (0.45), residues: 54 sheet: -0.15 (0.23), residues: 550 loop : -1.52 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 211 TYR 0.017 0.002 TYR C 33 PHE 0.019 0.002 PHE M 377 TRP 0.010 0.002 TRP A 47 HIS 0.005 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00480 (10142) covalent geometry : angle 0.68564 (13794) SS BOND : bond 0.00852 ( 14) SS BOND : angle 1.80062 ( 28) hydrogen bonds : bond 0.03771 ( 345) hydrogen bonds : angle 5.96385 ( 1008) link_BETA1-4 : bond 0.00039 ( 1) link_BETA1-4 : angle 1.69135 ( 3) link_BETA1-6 : bond 0.00346 ( 1) link_BETA1-6 : angle 1.71698 ( 3) link_NAG-ASN : bond 0.00295 ( 1) link_NAG-ASN : angle 1.75639 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 134 time to evaluate : 0.368 Fit side-chains REVERT: A 119 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8218 (pt0) REVERT: B 126 LYS cc_start: 0.7846 (mmtt) cc_final: 0.7550 (pttm) REVERT: B 145 LYS cc_start: 0.7662 (ttpt) cc_final: 0.7356 (ttpt) REVERT: B 169 LYS cc_start: 0.7405 (ttpt) cc_final: 0.6679 (mmmt) REVERT: B 183 LYS cc_start: 0.6443 (ptpt) cc_final: 0.6227 (ptpp) REVERT: B 188 LYS cc_start: 0.6971 (ttpt) cc_final: 0.6746 (ttmt) REVERT: C 109 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8201 (mp10) REVERT: D 27 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.7232 (tt0) REVERT: D 140 TYR cc_start: 0.7579 (t80) cc_final: 0.7090 (t80) REVERT: H 19 ARG cc_start: 0.7865 (ttt-90) cc_final: 0.7624 (tmt90) REVERT: M 339 ASP cc_start: 0.8733 (m-30) cc_final: 0.8462 (m-30) outliers start: 44 outliers final: 36 residues processed: 161 average time/residue: 0.5384 time to fit residues: 93.2224 Evaluate side-chains 158 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 376 THR Chi-restraints excluded: chain M residue 389 ASP Chi-restraints excluded: chain M residue 445 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 60 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN L 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.157020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.117436 restraints weight = 14758.936| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.27 r_work: 0.3364 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10159 Z= 0.224 Angle : 0.717 7.597 13831 Z= 0.371 Chirality : 0.048 0.231 1545 Planarity : 0.007 0.104 1765 Dihedral : 5.928 54.586 1465 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.92 % Favored : 91.92 % Rotamer: Outliers : 4.27 % Allowed : 16.09 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 1.52 % 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: -1.54 (0.23), residues: 1276 helix: -3.50 (0.48), residues: 54 sheet: -0.16 (0.23), residues: 551 loop : -1.56 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 211 TYR 0.018 0.002 TYR C 33 PHE 0.021 0.002 PHE M 377 TRP 0.010 0.002 TRP A 47 HIS 0.005 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00537 (10142) covalent geometry : angle 0.71156 (13794) SS BOND : bond 0.00924 ( 14) SS BOND : angle 1.94562 ( 28) hydrogen bonds : bond 0.03899 ( 345) hydrogen bonds : angle 6.01606 ( 1008) link_BETA1-4 : bond 0.00017 ( 1) link_BETA1-4 : angle 1.66798 ( 3) link_BETA1-6 : bond 0.00307 ( 1) link_BETA1-6 : angle 1.76091 ( 3) link_NAG-ASN : bond 0.00268 ( 1) link_NAG-ASN : angle 1.82122 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 120 time to evaluate : 0.344 Fit side-chains REVERT: A 119 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8186 (pt0) REVERT: B 126 LYS cc_start: 0.7873 (mmtt) cc_final: 0.7540 (pttm) REVERT: B 145 LYS cc_start: 0.7632 (ttpt) cc_final: 0.7328 (ttpt) REVERT: B 169 LYS cc_start: 0.7410 (ttpt) cc_final: 0.6674 (mmmt) REVERT: C 109 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8201 (mp10) REVERT: D 27 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.7218 (tt0) REVERT: D 140 TYR cc_start: 0.7497 (t80) cc_final: 0.6940 (t80) REVERT: H 19 ARG cc_start: 0.7860 (ttt-90) cc_final: 0.7617 (tmt90) REVERT: M 339 ASP cc_start: 0.8737 (m-30) cc_final: 0.8475 (m-30) outliers start: 46 outliers final: 40 residues processed: 148 average time/residue: 0.4871 time to fit residues: 78.0893 Evaluate side-chains 161 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 118 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 376 THR Chi-restraints excluded: chain M residue 389 ASP Chi-restraints excluded: chain M residue 445 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 76 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 111 optimal weight: 0.3980 chunk 84 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN H 39 GLN L 3 GLN L 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.159981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.120020 restraints weight = 17687.054| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.49 r_work: 0.3394 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10159 Z= 0.128 Angle : 0.632 7.403 13831 Z= 0.326 Chirality : 0.045 0.205 1545 Planarity : 0.006 0.098 1765 Dihedral : 5.569 53.749 1465 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.35 % Favored : 93.49 % Rotamer: Outliers : 3.18 % Allowed : 17.36 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % 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: -1.27 (0.23), residues: 1276 helix: -3.27 (0.55), residues: 47 sheet: 0.06 (0.23), residues: 537 loop : -1.42 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 211 TYR 0.015 0.001 TYR D 140 PHE 0.015 0.001 PHE D 139 TRP 0.014 0.001 TRP H 47 HIS 0.004 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00299 (10142) covalent geometry : angle 0.62906 (13794) SS BOND : bond 0.00596 ( 14) SS BOND : angle 1.25041 ( 28) hydrogen bonds : bond 0.03235 ( 345) hydrogen bonds : angle 5.69676 ( 1008) link_BETA1-4 : bond 0.00111 ( 1) link_BETA1-4 : angle 1.78788 ( 3) link_BETA1-6 : bond 0.00213 ( 1) link_BETA1-6 : angle 1.63155 ( 3) link_NAG-ASN : bond 0.00398 ( 1) link_NAG-ASN : angle 1.64782 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 0.324 Fit side-chains REVERT: A 119 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8352 (pt0) REVERT: B 126 LYS cc_start: 0.7855 (mmtt) cc_final: 0.7481 (pttm) REVERT: B 143 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7640 (mp0) REVERT: B 145 LYS cc_start: 0.7693 (ttpt) cc_final: 0.7430 (ttpt) REVERT: B 169 LYS cc_start: 0.7373 (ttpt) cc_final: 0.6659 (mmtt) REVERT: D 140 TYR cc_start: 0.7417 (t80) cc_final: 0.7071 (t80) REVERT: H 19 ARG cc_start: 0.7876 (ttt-90) cc_final: 0.7626 (tmt90) REVERT: M 339 ASP cc_start: 0.8713 (m-30) cc_final: 0.8444 (m-30) REVERT: M 357 ARG cc_start: 0.8520 (ttp-170) cc_final: 0.8049 (ttt-90) REVERT: M 389 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7358 (p0) REVERT: M 474 GLN cc_start: 0.7719 (pt0) cc_final: 0.7252 (tt0) outliers start: 34 outliers final: 22 residues processed: 161 average time/residue: 0.5578 time to fit residues: 96.0117 Evaluate side-chains 151 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 389 ASP Chi-restraints excluded: chain M residue 445 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 44 optimal weight: 0.0670 chunk 98 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.158472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.117219 restraints weight = 23586.821| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.86 r_work: 0.3341 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10159 Z= 0.188 Angle : 0.680 7.356 13831 Z= 0.351 Chirality : 0.046 0.234 1545 Planarity : 0.006 0.103 1765 Dihedral : 5.703 53.500 1465 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.37 % Favored : 92.47 % Rotamer: Outliers : 3.09 % Allowed : 17.91 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 1.52 % 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: -1.33 (0.23), residues: 1276 helix: -3.28 (0.52), residues: 54 sheet: 0.01 (0.23), residues: 543 loop : -1.45 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 211 TYR 0.016 0.002 TYR C 33 PHE 0.017 0.002 PHE M 377 TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00452 (10142) covalent geometry : angle 0.67524 (13794) SS BOND : bond 0.00816 ( 14) SS BOND : angle 1.74957 ( 28) hydrogen bonds : bond 0.03571 ( 345) hydrogen bonds : angle 5.80377 ( 1008) link_BETA1-4 : bond 0.00032 ( 1) link_BETA1-4 : angle 1.64062 ( 3) link_BETA1-6 : bond 0.00226 ( 1) link_BETA1-6 : angle 1.76866 ( 3) link_NAG-ASN : bond 0.00268 ( 1) link_NAG-ASN : angle 1.69674 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4975.83 seconds wall clock time: 85 minutes 9.14 seconds (5109.14 seconds total)