Starting phenix.real_space_refine on Wed Aug 5 06:38:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v1y_42892/08_2026/8v1y_42892.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v1y_42892/08_2026/8v1y_42892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8v1y_42892/08_2026/8v1y_42892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v1y_42892/08_2026/8v1y_42892.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v1y_42892/08_2026/8v1y_42892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v1y_42892/08_2026/8v1y_42892.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 50 5.16 5 C 5634 2.51 5 N 1545 2.21 5 O 1687 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8918 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3567 Classifications: {'peptide': 457} Link IDs: {'PTRANS': 25, 'TRANS': 431} Chain breaks: 3 Chain: "B" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3563 Classifications: {'peptide': 457} Link IDs: {'PTRANS': 25, 'TRANS': 431} Chain breaks: 2 Chain: "C" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 868 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 876 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 105} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'AMP%rna3p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna3p': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 1.86, per 1000 atoms: 0.21 Number of scatterers: 8918 At special positions: 0 Unit cell: (81.34, 141.93, 106.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 P 2 15.00 O 1687 8.00 N 1545 7.00 C 5634 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 258.3 milliseconds 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 13 sheets defined 40.9% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 removed outlier: 3.565A pdb=" N ASN A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 40 through 47 removed outlier: 3.798A pdb=" N PHE A 44 " --> pdb=" O ASN A 40 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 75 removed outlier: 3.560A pdb=" N ALA A 75 " --> pdb=" O ALA A 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 72 through 75' Processing helix chain 'A' and resid 104 through 120 removed outlier: 3.681A pdb=" N GLY A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 162 removed outlier: 3.572A pdb=" N SER A 161 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER A 162 " --> pdb=" O TRP A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 203 Processing helix chain 'A' and resid 229 through 250 Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 292 through 305 Processing helix chain 'A' and resid 305 through 314 removed outlier: 3.916A pdb=" N ALA A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 323 Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 367 through 386 Processing helix chain 'A' and resid 414 through 425 Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 436 through 457 removed outlier: 3.600A pdb=" N GLU A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 466 Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 40 through 47 removed outlier: 3.729A pdb=" N PHE B 44 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 75 Processing helix chain 'B' and resid 104 through 120 removed outlier: 3.658A pdb=" N GLY B 120 " --> pdb=" O LEU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 162 removed outlier: 3.710A pdb=" N SER B 161 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER B 162 " --> pdb=" O TRP B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 203 Processing helix chain 'B' and resid 229 through 250 Processing helix chain 'B' and resid 287 through 291 Processing helix chain 'B' and resid 292 through 314 removed outlier: 5.218A pdb=" N LYS B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ALA B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B 311 " --> pdb=" O LYS B 307 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 321 Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'B' and resid 367 through 386 Processing helix chain 'B' and resid 414 through 425 Processing helix chain 'B' and resid 430 through 434 removed outlier: 3.602A pdb=" N VAL B 434 " --> pdb=" O ALA B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 457 removed outlier: 3.541A pdb=" N THR B 457 " --> pdb=" O ARG B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 466 removed outlier: 3.679A pdb=" N PHE B 463 " --> pdb=" O HIS B 459 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU B 464 " --> pdb=" O PRO B 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 12 Processing helix chain 'C' and resid 50 through 54 Processing helix chain 'C' and resid 55 through 58 Processing helix chain 'C' and resid 59 through 77 removed outlier: 4.302A pdb=" N GLY C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG C 64 " --> pdb=" O GLN C 60 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE C 66 " --> pdb=" O LEU C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 94 Processing helix chain 'D' and resid 5 through 12 Processing helix chain 'D' and resid 50 through 54 Processing helix chain 'D' and resid 58 through 77 removed outlier: 3.507A pdb=" N LEU D 62 " --> pdb=" O HIS D 58 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY D 63 " --> pdb=" O GLU D 59 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 35 removed outlier: 6.942A pdb=" N PHE A 17 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE A 88 " --> pdb=" O PHE A 17 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ASP A 19 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N CYS A 90 " --> pdb=" O ASP A 19 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ARG A 21 " --> pdb=" O CYS A 90 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE A 92 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 9.840A pdb=" N THR A 23 " --> pdb=" O ILE A 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 35 removed outlier: 6.942A pdb=" N PHE A 17 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE A 88 " --> pdb=" O PHE A 17 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ASP A 19 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N CYS A 90 " --> pdb=" O ASP A 19 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ARG A 21 " --> pdb=" O CYS A 90 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE A 92 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 9.840A pdb=" N THR A 23 " --> pdb=" O ILE A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 228 Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 228 removed outlier: 7.740A pdb=" N MET A 332 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ARG A 345 " --> pdb=" O MET A 332 " (cutoff:3.500A) removed outlier: 10.350A pdb=" N ALA A 334 " --> pdb=" O ARG A 345 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 207 through 212 removed outlier: 3.901A pdb=" N ALA A 209 " --> pdb=" O ALA A 223 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 138 through 144 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 35 removed outlier: 6.941A pdb=" N PHE B 17 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ILE B 88 " --> pdb=" O PHE B 17 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASP B 19 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N CYS B 90 " --> pdb=" O ASP B 19 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ARG B 21 " --> pdb=" O CYS B 90 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ILE B 92 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 9.907A pdb=" N THR B 23 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 29 through 35 removed outlier: 6.941A pdb=" N PHE B 17 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ILE B 88 " --> pdb=" O PHE B 17 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASP B 19 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N CYS B 90 " --> pdb=" O ASP B 19 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ARG B 21 " --> pdb=" O CYS B 90 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ILE B 92 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 9.907A pdb=" N THR B 23 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 227 through 228 Processing sheet with id=AB1, first strand: chain 'B' and resid 227 through 228 removed outlier: 7.572A pdb=" N MET B 332 " --> pdb=" O SER B 343 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ARG B 345 " --> pdb=" O MET B 332 " (cutoff:3.500A) removed outlier: 10.411A pdb=" N ALA B 334 " --> pdb=" O ARG B 345 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 207 through 212 removed outlier: 3.809A pdb=" N ALA B 209 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 138 through 144 Processing sheet with id=AB4, first strand: chain 'C' and resid 19 through 22 removed outlier: 6.371A pdb=" N ALA C 28 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLN C 22 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL C 26 " --> pdb=" O GLN C 22 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR D 83 " --> pdb=" O THR C 89 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR D 38 " --> pdb=" O GLY D 106 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ALA D 28 " --> pdb=" O VAL D 20 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1140 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: 1.66 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2996 1.34 - 1.46: 1585 1.46 - 1.57: 4439 1.57 - 1.69: 2 1.69 - 1.81: 92 Bond restraints: 9114 Sorted by residual: bond pdb=" C4 AMP A 501 " pdb=" C5 AMP A 501 " ideal model delta sigma weight residual 1.490 1.376 0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" C4 AMP B 501 " pdb=" C5 AMP B 501 " ideal model delta sigma weight residual 1.490 1.376 0.114 2.00e-02 2.50e+03 3.24e+01 bond pdb=" C5 AMP A 501 " pdb=" C6 AMP A 501 " ideal model delta sigma weight residual 1.490 1.404 0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C5 AMP B 501 " pdb=" C6 AMP B 501 " ideal model delta sigma weight residual 1.490 1.404 0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C8 AMP B 501 " pdb=" N7 AMP B 501 " ideal model delta sigma weight residual 1.350 1.307 0.043 2.00e-02 2.50e+03 4.68e+00 ... (remaining 9109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 12187 1.87 - 3.74: 125 3.74 - 5.61: 19 5.61 - 7.48: 4 7.48 - 9.34: 4 Bond angle restraints: 12339 Sorted by residual: angle pdb=" N VAL D 97 " pdb=" CA VAL D 97 " pdb=" C VAL D 97 " ideal model delta sigma weight residual 112.96 109.12 3.84 1.00e+00 1.00e+00 1.47e+01 angle pdb=" N1 AMP B 501 " pdb=" C2 AMP B 501 " pdb=" N3 AMP B 501 " ideal model delta sigma weight residual 120.00 129.34 -9.34 3.00e+00 1.11e-01 9.70e+00 angle pdb=" N1 AMP A 501 " pdb=" C2 AMP A 501 " pdb=" N3 AMP A 501 " ideal model delta sigma weight residual 120.00 129.25 -9.25 3.00e+00 1.11e-01 9.50e+00 angle pdb=" C2 AMP A 501 " pdb=" N3 AMP A 501 " pdb=" C4 AMP A 501 " ideal model delta sigma weight residual 120.00 110.80 9.20 3.00e+00 1.11e-01 9.40e+00 angle pdb=" C2 AMP B 501 " pdb=" N3 AMP B 501 " pdb=" C4 AMP B 501 " ideal model delta sigma weight residual 120.00 110.81 9.19 3.00e+00 1.11e-01 9.38e+00 ... (remaining 12334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 5011 17.40 - 34.81: 391 34.81 - 52.21: 53 52.21 - 69.61: 18 69.61 - 87.02: 6 Dihedral angle restraints: 5479 sinusoidal: 2206 harmonic: 3273 Sorted by residual: dihedral pdb=" C1' AMP A 501 " pdb=" C4' AMP A 501 " pdb=" O4' AMP A 501 " pdb=" C5' AMP A 501 " ideal model delta sinusoidal sigma weight residual -123.00 -159.56 36.56 1 8.00e+00 1.56e-02 2.95e+01 dihedral pdb=" CA THR B 228 " pdb=" C THR B 228 " pdb=" N MET B 229 " pdb=" CA MET B 229 " ideal model delta harmonic sigma weight residual -180.00 -162.71 -17.29 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA TYR A 320 " pdb=" C TYR A 320 " pdb=" N LYS A 321 " pdb=" CA LYS A 321 " ideal model delta harmonic sigma weight residual 180.00 163.13 16.87 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 5476 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 853 0.031 - 0.062: 326 0.062 - 0.093: 97 0.093 - 0.123: 69 0.123 - 0.154: 11 Chirality restraints: 1356 Sorted by residual: chirality pdb=" C2' AMP B 501 " pdb=" C1' AMP B 501 " pdb=" C3' AMP B 501 " pdb=" O2' AMP B 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.60 -0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA PHE B 361 " pdb=" N PHE B 361 " pdb=" C PHE B 361 " pdb=" CB PHE B 361 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.82e-01 chirality pdb=" CA VAL A 324 " pdb=" N VAL A 324 " pdb=" C VAL A 324 " pdb=" CB VAL A 324 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.60e-01 ... (remaining 1353 not shown) Planarity restraints: 1617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 314 " -0.034 5.00e-02 4.00e+02 5.20e-02 4.32e+00 pdb=" N PRO B 315 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 315 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 315 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 128 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.87e+00 pdb=" N PRO B 129 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 129 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 129 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 184 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A 185 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 185 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 185 " 0.023 5.00e-02 4.00e+02 ... (remaining 1614 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2071 2.79 - 3.32: 8365 3.32 - 3.85: 14654 3.85 - 4.37: 17539 4.37 - 4.90: 29674 Nonbonded interactions: 72303 Sorted by model distance: nonbonded pdb=" OG SER B 319 " pdb=" OD2 ASP B 363 " model vdw 2.268 3.040 nonbonded pdb=" NH2 ARG D 84 " pdb=" O GLY D 111 " model vdw 2.277 3.120 nonbonded pdb=" OG1 THR B 316 " pdb=" OG SER B 319 " model vdw 2.282 3.040 nonbonded pdb=" O ASN C 88 " pdb=" NE2 GLN C 95 " model vdw 2.294 3.120 nonbonded pdb=" OE2 GLU B 416 " pdb=" NH1 ARG B 448 " model vdw 2.301 3.120 ... (remaining 72298 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 398 or resid 406 through 501)) selection = (chain 'B' and (resid 1 through 59 or resid 62 through 501)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 3 through 30 or resid 32 through 116)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.260 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.010 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:8.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 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 : 0.003 0.114 9116 Z= 0.182 Angle : 0.516 9.344 12339 Z= 0.259 Chirality : 0.042 0.154 1356 Planarity : 0.004 0.052 1617 Dihedral : 12.809 87.017 3371 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.13 (0.25), residues: 1113 helix: 1.45 (0.27), residues: 376 sheet: 1.13 (0.34), residues: 224 loop : 0.14 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 103 TYR 0.011 0.001 TYR B 239 PHE 0.016 0.001 PHE B 361 TRP 0.001 0.000 TRP B 58 HIS 0.003 0.000 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 ( 9114) covalent geometry : angle 0.51558 / 0.26 (12339) hydrogen bonds : bond 0.17194 / 11.59 ( 406) hydrogen bonds : angle 6.86188 / 4.82 ( 1140) Misc. bond : bond 0.06274 / 3.14 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 SER cc_start: 0.8110 (t) cc_final: 0.7806 (p) REVERT: A 4 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8165 (mp0) REVERT: A 12 GLU cc_start: 0.8530 (tt0) cc_final: 0.8315 (tt0) REVERT: A 42 GLU cc_start: 0.8762 (pp20) cc_final: 0.8495 (pp20) REVERT: A 154 ASP cc_start: 0.8342 (p0) cc_final: 0.8008 (p0) REVERT: A 155 ILE cc_start: 0.8595 (mt) cc_final: 0.8381 (tp) REVERT: A 338 ARG cc_start: 0.9025 (mtt180) cc_final: 0.8752 (mtt180) REVERT: A 437 ASP cc_start: 0.8675 (t70) cc_final: 0.8357 (m-30) REVERT: A 441 ASP cc_start: 0.8915 (m-30) cc_final: 0.8648 (m-30) REVERT: B 32 VAL cc_start: 0.8734 (t) cc_final: 0.8528 (p) REVERT: B 42 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8653 (mt-10) REVERT: B 137 ASP cc_start: 0.8780 (m-30) cc_final: 0.8483 (m-30) REVERT: B 155 ILE cc_start: 0.8506 (mt) cc_final: 0.8285 (tp) REVERT: B 277 LYS cc_start: 0.8808 (tttt) cc_final: 0.8543 (tttp) REVERT: B 345 ARG cc_start: 0.8820 (mmm160) cc_final: 0.8477 (mmm-85) REVERT: B 353 LYS cc_start: 0.9120 (mttt) cc_final: 0.8907 (mttt) REVERT: B 416 GLU cc_start: 0.8783 (tp30) cc_final: 0.8562 (tt0) REVERT: B 425 ASP cc_start: 0.8611 (t0) cc_final: 0.8069 (t0) REVERT: B 450 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7810 (mt-10) REVERT: C 90 ASN cc_start: 0.8460 (m110) cc_final: 0.8259 (m110) REVERT: D 76 GLU cc_start: 0.9067 (tp30) cc_final: 0.8840 (tp30) outliers start: 0 outliers final: 1 residues processed: 314 average time/residue: 0.6458 time to fit residues: 214.2704 Evaluate side-chains 242 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 241 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 357 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 HIS A 212 HIS ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN B 160 ASN C 35 GLN D 35 GLN ** D 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.138319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.126565 restraints weight = 14311.098| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.01 r_work: 0.3539 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 9116 Z= 0.318 Angle : 0.643 7.923 12339 Z= 0.339 Chirality : 0.050 0.206 1356 Planarity : 0.006 0.054 1617 Dihedral : 5.084 44.031 1243 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.80 % Allowed : 13.53 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.76 (0.25), residues: 1113 helix: 1.24 (0.27), residues: 375 sheet: 1.14 (0.36), residues: 205 loop : -0.23 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 108 TYR 0.018 0.002 TYR B 239 PHE 0.023 0.002 PHE A 361 TRP 0.006 0.002 TRP B 159 HIS 0.005 0.001 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00728 / 0.32 ( 9114) covalent geometry : angle 0.64307 / 0.34 (12339) hydrogen bonds : bond 0.05178 / 3.42 ( 406) hydrogen bonds : angle 5.51860 / 3.89 ( 1140) Misc. bond : bond 0.00183 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 258 time to evaluate : 0.357 Fit side-chains REVERT: A 2 SER cc_start: 0.7866 (t) cc_final: 0.7604 (p) REVERT: A 4 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7650 (mp0) REVERT: A 12 GLU cc_start: 0.7692 (tt0) cc_final: 0.7425 (tt0) REVERT: A 42 GLU cc_start: 0.7961 (pp20) cc_final: 0.7431 (pp20) REVERT: A 155 ILE cc_start: 0.8510 (mt) cc_final: 0.8264 (tp) REVERT: A 269 MET cc_start: 0.8721 (ttp) cc_final: 0.8423 (ttp) REVERT: A 276 SER cc_start: 0.8597 (m) cc_final: 0.8220 (t) REVERT: B 10 LEU cc_start: 0.8462 (mt) cc_final: 0.8255 (mp) REVERT: B 32 VAL cc_start: 0.8479 (t) cc_final: 0.8272 (p) REVERT: B 42 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7961 (mt-10) REVERT: B 54 SER cc_start: 0.8662 (t) cc_final: 0.8448 (m) REVERT: B 177 LYS cc_start: 0.8494 (mtpt) cc_final: 0.7921 (mtmm) REVERT: B 277 LYS cc_start: 0.8718 (tttt) cc_final: 0.8453 (tttp) REVERT: B 345 ARG cc_start: 0.8229 (mmm160) cc_final: 0.7934 (mmm-85) REVERT: B 398 TYR cc_start: 0.8823 (m-80) cc_final: 0.7590 (m-80) REVERT: B 425 ASP cc_start: 0.8037 (t0) cc_final: 0.7669 (t0) REVERT: C 90 ASN cc_start: 0.8366 (m110) cc_final: 0.8149 (m110) REVERT: D 65 MET cc_start: 0.7156 (mtt) cc_final: 0.6926 (mtt) REVERT: D 102 MET cc_start: 0.8155 (ttp) cc_final: 0.7791 (mtp) outliers start: 17 outliers final: 12 residues processed: 263 average time/residue: 0.6394 time to fit residues: 177.9543 Evaluate side-chains 254 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 242 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 58 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 29 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 59 optimal weight: 0.1980 chunk 39 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 GLN C 116 HIS D 35 GLN ** D 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.140505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.128735 restraints weight = 14223.452| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.01 r_work: 0.3575 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9116 Z= 0.131 Angle : 0.559 8.417 12339 Z= 0.288 Chirality : 0.045 0.181 1356 Planarity : 0.005 0.059 1617 Dihedral : 5.071 53.107 1243 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.59 % Allowed : 18.39 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.78 (0.25), residues: 1113 helix: 1.41 (0.27), residues: 376 sheet: 1.11 (0.36), residues: 207 loop : -0.33 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 30 TYR 0.013 0.001 TYR B 239 PHE 0.022 0.001 PHE B 361 TRP 0.004 0.001 TRP A 159 HIS 0.007 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 9114) covalent geometry : angle 0.55869 / 0.29 (12339) hydrogen bonds : bond 0.03952 / 2.64 ( 406) hydrogen bonds : angle 5.10057 / 3.61 ( 1140) Misc. bond : bond 0.00065 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 257 time to evaluate : 0.365 Fit side-chains REVERT: A 2 SER cc_start: 0.7838 (t) cc_final: 0.7543 (p) REVERT: A 4 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7633 (mp0) REVERT: A 12 GLU cc_start: 0.7651 (tt0) cc_final: 0.7402 (tt0) REVERT: A 33 THR cc_start: 0.7977 (t) cc_final: 0.7708 (m) REVERT: A 42 GLU cc_start: 0.7891 (pp20) cc_final: 0.7375 (pp20) REVERT: A 55 ILE cc_start: 0.8699 (mm) cc_final: 0.8370 (mt) REVERT: A 154 ASP cc_start: 0.7698 (p0) cc_final: 0.7323 (t70) REVERT: A 155 ILE cc_start: 0.8522 (mt) cc_final: 0.8049 (tp) REVERT: A 276 SER cc_start: 0.8560 (m) cc_final: 0.8162 (t) REVERT: A 338 ARG cc_start: 0.8090 (mtt180) cc_final: 0.7822 (mtt90) REVERT: A 441 ASP cc_start: 0.8168 (m-30) cc_final: 0.7737 (m-30) REVERT: B 10 LEU cc_start: 0.8465 (mt) cc_final: 0.8251 (mp) REVERT: B 42 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7946 (mt-10) REVERT: B 49 MET cc_start: 0.8582 (mtp) cc_final: 0.8353 (mmm) REVERT: B 110 LYS cc_start: 0.8546 (mttp) cc_final: 0.8337 (mttt) REVERT: B 137 ASP cc_start: 0.8058 (m-30) cc_final: 0.7804 (m-30) REVERT: B 177 LYS cc_start: 0.8397 (mtpt) cc_final: 0.7853 (mtmm) REVERT: B 277 LYS cc_start: 0.8681 (tttt) cc_final: 0.8423 (tttp) REVERT: B 332 MET cc_start: 0.8155 (mmm) cc_final: 0.7945 (tpp) REVERT: B 338 ARG cc_start: 0.8081 (mtt180) cc_final: 0.7847 (mtp-110) REVERT: B 345 ARG cc_start: 0.8231 (mmm160) cc_final: 0.7953 (mmm-85) REVERT: B 398 TYR cc_start: 0.8741 (m-80) cc_final: 0.7384 (m-10) REVERT: B 425 ASP cc_start: 0.8079 (t0) cc_final: 0.7747 (t0) REVERT: B 438 GLU cc_start: 0.8059 (mp0) cc_final: 0.7833 (mp0) REVERT: B 461 VAL cc_start: 0.8787 (t) cc_final: 0.8580 (m) REVERT: C 90 ASN cc_start: 0.8324 (m110) cc_final: 0.8114 (m110) REVERT: C 108 ARG cc_start: 0.8127 (ptt-90) cc_final: 0.7867 (ptt-90) REVERT: D 76 GLU cc_start: 0.8172 (tp30) cc_final: 0.7953 (tp30) outliers start: 15 outliers final: 10 residues processed: 260 average time/residue: 0.6227 time to fit residues: 171.7657 Evaluate side-chains 257 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 247 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 100 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 51 optimal weight: 5.9990 chunk 52 optimal weight: 0.0470 chunk 64 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 ASN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 HIS ** D 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.139367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.127684 restraints weight = 14347.398| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.01 r_work: 0.3556 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9116 Z= 0.194 Angle : 0.590 8.954 12339 Z= 0.303 Chirality : 0.046 0.182 1356 Planarity : 0.005 0.062 1617 Dihedral : 5.108 52.375 1243 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.96 % Allowed : 18.71 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.72 (0.25), residues: 1113 helix: 1.41 (0.27), residues: 375 sheet: 1.04 (0.37), residues: 205 loop : -0.38 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 453 TYR 0.016 0.001 TYR B 239 PHE 0.020 0.001 PHE B 361 TRP 0.005 0.001 TRP A 159 HIS 0.006 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 ( 9114) covalent geometry : angle 0.58987 / 0.30 (12339) hydrogen bonds : bond 0.04200 / 2.77 ( 406) hydrogen bonds : angle 5.09642 / 3.59 ( 1140) Misc. bond : bond 0.00098 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 252 time to evaluate : 0.252 Fit side-chains REVERT: A 2 SER cc_start: 0.7836 (t) cc_final: 0.7580 (p) REVERT: A 4 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7577 (mt-10) REVERT: A 12 GLU cc_start: 0.7700 (tt0) cc_final: 0.7438 (tt0) REVERT: A 33 THR cc_start: 0.8039 (t) cc_final: 0.7778 (m) REVERT: A 42 GLU cc_start: 0.7925 (pp20) cc_final: 0.7405 (pp20) REVERT: A 155 ILE cc_start: 0.8518 (mt) cc_final: 0.8063 (tp) REVERT: A 269 MET cc_start: 0.8739 (ttp) cc_final: 0.8440 (ttp) REVERT: A 276 SER cc_start: 0.8586 (m) cc_final: 0.8174 (t) REVERT: A 338 ARG cc_start: 0.8093 (mtt180) cc_final: 0.7816 (mtt90) REVERT: B 10 LEU cc_start: 0.8481 (mt) cc_final: 0.8261 (mp) REVERT: B 16 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8506 (mmmm) REVERT: B 42 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7977 (mt-10) REVERT: B 54 SER cc_start: 0.8653 (t) cc_final: 0.8429 (m) REVERT: B 177 LYS cc_start: 0.8399 (mtpt) cc_final: 0.8115 (mtmm) REVERT: B 338 ARG cc_start: 0.8093 (mtt180) cc_final: 0.7868 (mtp-110) REVERT: B 345 ARG cc_start: 0.8244 (mmm160) cc_final: 0.7973 (mmm-85) REVERT: B 398 TYR cc_start: 0.8769 (m-80) cc_final: 0.7455 (m-80) REVERT: B 425 ASP cc_start: 0.8080 (t0) cc_final: 0.7723 (t0) REVERT: B 429 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7851 (pt) REVERT: B 438 GLU cc_start: 0.8069 (mp0) cc_final: 0.7833 (mp0) REVERT: C 90 ASN cc_start: 0.8348 (m110) cc_final: 0.8135 (m110) REVERT: D 102 MET cc_start: 0.8130 (ttp) cc_final: 0.7915 (mtp) outliers start: 28 outliers final: 13 residues processed: 261 average time/residue: 0.6185 time to fit residues: 170.7311 Evaluate side-chains 266 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 251 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 100 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 48 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.0370 chunk 95 optimal weight: 0.0020 chunk 109 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 overall best weight: 0.4466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN C 116 HIS ** D 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.141571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.130137 restraints weight = 14376.876| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.00 r_work: 0.3585 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9116 Z= 0.121 Angle : 0.566 8.851 12339 Z= 0.290 Chirality : 0.044 0.195 1356 Planarity : 0.005 0.064 1617 Dihedral : 5.078 54.958 1243 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.64 % Allowed : 19.98 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.83 (0.25), residues: 1113 helix: 1.55 (0.27), residues: 376 sheet: 1.06 (0.37), residues: 205 loop : -0.35 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 453 TYR 0.013 0.001 TYR B 239 PHE 0.028 0.001 PHE A 361 TRP 0.004 0.001 TRP A 159 HIS 0.005 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 9114) covalent geometry : angle 0.56561 / 0.29 (12339) hydrogen bonds : bond 0.03590 / 2.38 ( 406) hydrogen bonds : angle 4.89039 / 3.44 ( 1140) Misc. bond : bond 0.00060 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 253 time to evaluate : 0.302 Fit side-chains REVERT: A 4 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7604 (mp0) REVERT: A 12 GLU cc_start: 0.7647 (tt0) cc_final: 0.7381 (tt0) REVERT: A 33 THR cc_start: 0.7978 (t) cc_final: 0.7700 (m) REVERT: A 42 GLU cc_start: 0.7872 (pp20) cc_final: 0.7350 (pp20) REVERT: A 51 ASP cc_start: 0.8237 (t70) cc_final: 0.7852 (t0) REVERT: A 55 ILE cc_start: 0.8731 (mm) cc_final: 0.8412 (mt) REVERT: A 113 GLU cc_start: 0.8264 (mt-10) cc_final: 0.8064 (mt-10) REVERT: A 269 MET cc_start: 0.8725 (ttp) cc_final: 0.8433 (ttp) REVERT: A 276 SER cc_start: 0.8548 (m) cc_final: 0.8142 (t) REVERT: A 338 ARG cc_start: 0.8080 (mtt180) cc_final: 0.7837 (mtt90) REVERT: A 441 ASP cc_start: 0.8143 (m-30) cc_final: 0.7813 (m-30) REVERT: B 16 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8461 (mmmm) REVERT: B 42 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8004 (mt-10) REVERT: B 110 LYS cc_start: 0.8595 (mttp) cc_final: 0.8393 (mttt) REVERT: B 177 LYS cc_start: 0.8370 (mtpt) cc_final: 0.8081 (mtmm) REVERT: B 338 ARG cc_start: 0.8070 (mtt180) cc_final: 0.7828 (mtp-110) REVERT: B 345 ARG cc_start: 0.8226 (mmm160) cc_final: 0.7930 (mmm-85) REVERT: B 398 TYR cc_start: 0.8711 (m-80) cc_final: 0.7245 (m-80) REVERT: B 425 ASP cc_start: 0.8096 (t0) cc_final: 0.7837 (t0) REVERT: C 90 ASN cc_start: 0.8276 (m110) cc_final: 0.8059 (m110) outliers start: 25 outliers final: 13 residues processed: 262 average time/residue: 0.6409 time to fit residues: 177.6341 Evaluate side-chains 262 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 248 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain D residue 50 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 33 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 35 GLN ** D 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.136967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.125555 restraints weight = 14398.852| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.98 r_work: 0.3529 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9116 Z= 0.283 Angle : 0.653 9.524 12339 Z= 0.338 Chirality : 0.048 0.219 1356 Planarity : 0.006 0.067 1617 Dihedral : 5.238 48.613 1243 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.85 % Allowed : 20.51 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.62 (0.25), residues: 1113 helix: 1.36 (0.27), residues: 377 sheet: 0.94 (0.37), residues: 209 loop : -0.47 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 193 TYR 0.019 0.002 TYR B 239 PHE 0.030 0.002 PHE A 361 TRP 0.006 0.002 TRP B 159 HIS 0.005 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.28 ( 9114) covalent geometry : angle 0.65273 / 0.34 (12339) hydrogen bonds : bond 0.04614 / 3.02 ( 406) hydrogen bonds : angle 5.26358 / 3.71 ( 1140) Misc. bond : bond 0.00114 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 245 time to evaluate : 0.354 Fit side-chains REVERT: A 2 SER cc_start: 0.7801 (t) cc_final: 0.7523 (p) REVERT: A 4 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7567 (mt-10) REVERT: A 12 GLU cc_start: 0.7748 (tt0) cc_final: 0.7469 (tt0) REVERT: A 42 GLU cc_start: 0.7932 (pp20) cc_final: 0.7413 (pp20) REVERT: A 269 MET cc_start: 0.8697 (ttp) cc_final: 0.8479 (ttp) REVERT: A 276 SER cc_start: 0.8561 (m) cc_final: 0.8163 (t) REVERT: A 338 ARG cc_start: 0.8089 (mtt180) cc_final: 0.7839 (mtt90) REVERT: B 42 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8018 (mt-10) REVERT: B 54 SER cc_start: 0.8660 (OUTLIER) cc_final: 0.8452 (m) REVERT: B 177 LYS cc_start: 0.8416 (mtpt) cc_final: 0.8138 (mtmm) REVERT: B 330 PRO cc_start: 0.8791 (Cg_endo) cc_final: 0.8453 (Cg_exo) REVERT: B 338 ARG cc_start: 0.8106 (mtt180) cc_final: 0.7873 (mtp-110) REVERT: B 345 ARG cc_start: 0.8217 (mmm160) cc_final: 0.7933 (mmm-85) REVERT: B 398 TYR cc_start: 0.8820 (m-80) cc_final: 0.7339 (m-80) REVERT: B 425 ASP cc_start: 0.8117 (t0) cc_final: 0.7729 (t0) REVERT: C 90 ASN cc_start: 0.8343 (m110) cc_final: 0.8113 (m110) outliers start: 27 outliers final: 14 residues processed: 253 average time/residue: 0.5842 time to fit residues: 156.5245 Evaluate side-chains 257 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 242 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 395 LYS Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 51 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 96 optimal weight: 4.9990 chunk 15 optimal weight: 0.0970 chunk 22 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.139100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.127764 restraints weight = 14438.870| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.99 r_work: 0.3561 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9116 Z= 0.143 Angle : 0.612 9.113 12339 Z= 0.315 Chirality : 0.045 0.194 1356 Planarity : 0.006 0.070 1617 Dihedral : 5.228 51.897 1243 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.75 % Allowed : 21.35 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.61 (0.25), residues: 1113 helix: 1.38 (0.27), residues: 381 sheet: 0.95 (0.37), residues: 205 loop : -0.51 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 108 TYR 0.016 0.001 TYR A 320 PHE 0.026 0.001 PHE A 361 TRP 0.005 0.001 TRP A 159 HIS 0.004 0.001 HIS C 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 9114) covalent geometry : angle 0.61174 / 0.31 (12339) hydrogen bonds : bond 0.03874 / 2.55 ( 406) hydrogen bonds : angle 5.11252 / 3.59 ( 1140) Misc. bond : bond 0.00060 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 245 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7609 (mp0) REVERT: A 12 GLU cc_start: 0.7690 (tt0) cc_final: 0.7413 (tt0) REVERT: A 33 THR cc_start: 0.8016 (t) cc_final: 0.7754 (m) REVERT: A 42 GLU cc_start: 0.7918 (pp20) cc_final: 0.7412 (pp20) REVERT: A 55 ILE cc_start: 0.8752 (mm) cc_final: 0.8452 (mt) REVERT: A 113 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8078 (mt-10) REVERT: A 276 SER cc_start: 0.8548 (m) cc_final: 0.8132 (t) REVERT: A 338 ARG cc_start: 0.8128 (mtt180) cc_final: 0.7892 (mtt90) REVERT: A 441 ASP cc_start: 0.8164 (m-30) cc_final: 0.7837 (m-30) REVERT: B 16 LYS cc_start: 0.8620 (mtpp) cc_final: 0.8394 (mmmm) REVERT: B 42 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7995 (mt-10) REVERT: B 54 SER cc_start: 0.8637 (OUTLIER) cc_final: 0.8418 (m) REVERT: B 177 LYS cc_start: 0.8377 (mtpt) cc_final: 0.8091 (mtmm) REVERT: B 277 LYS cc_start: 0.8623 (tttt) cc_final: 0.8386 (tttp) REVERT: B 330 PRO cc_start: 0.8752 (Cg_endo) cc_final: 0.8409 (Cg_exo) REVERT: B 332 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7915 (tpp) REVERT: B 338 ARG cc_start: 0.8099 (mtt180) cc_final: 0.7873 (mtp-110) REVERT: B 345 ARG cc_start: 0.8233 (mmm160) cc_final: 0.7939 (mmm-85) REVERT: B 398 TYR cc_start: 0.8679 (m-80) cc_final: 0.7352 (m-80) REVERT: B 425 ASP cc_start: 0.8145 (t0) cc_final: 0.7766 (t0) REVERT: C 90 ASN cc_start: 0.8292 (m110) cc_final: 0.8066 (m110) REVERT: D 102 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7372 (mtp) outliers start: 26 outliers final: 13 residues processed: 254 average time/residue: 0.5695 time to fit residues: 152.9053 Evaluate side-chains 264 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 248 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 102 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 87 optimal weight: 0.0050 chunk 84 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 27 optimal weight: 0.0670 chunk 74 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 17 optimal weight: 0.0770 chunk 24 optimal weight: 0.0030 overall best weight: 0.2100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 459 HIS ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN ** D 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.142316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.130909 restraints weight = 14323.872| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.00 r_work: 0.3595 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9116 Z= 0.110 Angle : 0.588 9.268 12339 Z= 0.299 Chirality : 0.043 0.159 1356 Planarity : 0.005 0.064 1617 Dihedral : 5.150 53.391 1243 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.69 % Allowed : 21.99 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.86 (0.25), residues: 1113 helix: 1.67 (0.27), residues: 376 sheet: 0.96 (0.36), residues: 209 loop : -0.37 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 108 TYR 0.016 0.001 TYR A 320 PHE 0.019 0.001 PHE A 361 TRP 0.003 0.000 TRP A 159 HIS 0.004 0.001 HIS C 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 9114) covalent geometry : angle 0.58817 / 0.30 (12339) hydrogen bonds : bond 0.03482 / 2.29 ( 406) hydrogen bonds : angle 4.90800 / 3.43 ( 1140) Misc. bond : bond 0.00060 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 254 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7606 (mp0) REVERT: A 33 THR cc_start: 0.7959 (t) cc_final: 0.7677 (m) REVERT: A 42 GLU cc_start: 0.7858 (pp20) cc_final: 0.7346 (pp20) REVERT: A 51 ASP cc_start: 0.8210 (t70) cc_final: 0.7800 (t0) REVERT: A 55 ILE cc_start: 0.8720 (mm) cc_final: 0.8405 (mt) REVERT: A 153 ASP cc_start: 0.8069 (t70) cc_final: 0.7867 (t0) REVERT: A 276 SER cc_start: 0.8496 (m) cc_final: 0.8109 (t) REVERT: A 338 ARG cc_start: 0.8067 (mtt180) cc_final: 0.7854 (mtt90) REVERT: A 441 ASP cc_start: 0.8097 (m-30) cc_final: 0.7815 (m-30) REVERT: B 16 LYS cc_start: 0.8605 (mtpp) cc_final: 0.8394 (mmmm) REVERT: B 42 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7967 (mt-10) REVERT: B 49 MET cc_start: 0.8407 (mmm) cc_final: 0.8207 (mmm) REVERT: B 177 LYS cc_start: 0.8307 (mtpt) cc_final: 0.8013 (mtmm) REVERT: B 330 PRO cc_start: 0.8766 (Cg_endo) cc_final: 0.8403 (Cg_exo) REVERT: B 332 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7914 (tpp) REVERT: B 338 ARG cc_start: 0.8110 (mtt180) cc_final: 0.7879 (mtp-110) REVERT: B 345 ARG cc_start: 0.8191 (mmm160) cc_final: 0.7896 (mmm-85) REVERT: B 398 TYR cc_start: 0.8657 (m-80) cc_final: 0.7285 (m-80) REVERT: B 425 ASP cc_start: 0.8136 (t0) cc_final: 0.7908 (t0) REVERT: B 461 VAL cc_start: 0.8809 (t) cc_final: 0.8586 (m) REVERT: C 90 ASN cc_start: 0.8229 (m110) cc_final: 0.8001 (m110) outliers start: 16 outliers final: 8 residues processed: 257 average time/residue: 0.5273 time to fit residues: 143.3890 Evaluate side-chains 255 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 246 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 395 LYS Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain D residue 10 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 55 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 104 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.139658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.128219 restraints weight = 14225.191| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.98 r_work: 0.3559 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9116 Z= 0.180 Angle : 0.654 10.903 12339 Z= 0.333 Chirality : 0.045 0.188 1356 Planarity : 0.006 0.069 1617 Dihedral : 5.201 48.856 1241 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.01 % Allowed : 22.52 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.84 (0.25), residues: 1113 helix: 1.60 (0.27), residues: 375 sheet: 0.95 (0.36), residues: 213 loop : -0.33 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 108 TYR 0.016 0.001 TYR A 320 PHE 0.025 0.001 PHE B 361 TRP 0.004 0.001 TRP B 159 HIS 0.006 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 ( 9114) covalent geometry : angle 0.65410 / 0.33 (12339) hydrogen bonds : bond 0.03932 / 2.58 ( 406) hydrogen bonds : angle 5.05694 / 3.54 ( 1140) Misc. bond : bond 0.00104 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 243 time to evaluate : 0.204 Fit side-chains REVERT: A 4 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7661 (mp0) REVERT: A 33 THR cc_start: 0.8029 (t) cc_final: 0.7773 (m) REVERT: A 42 GLU cc_start: 0.7893 (pp20) cc_final: 0.7389 (pp20) REVERT: A 51 ASP cc_start: 0.8213 (t70) cc_final: 0.7830 (t0) REVERT: A 55 ILE cc_start: 0.8739 (mm) cc_final: 0.8432 (mt) REVERT: A 276 SER cc_start: 0.8527 (m) cc_final: 0.8103 (t) REVERT: A 338 ARG cc_start: 0.8083 (mtt180) cc_final: 0.7854 (mtt90) REVERT: A 441 ASP cc_start: 0.8128 (m-30) cc_final: 0.7813 (m-30) REVERT: B 16 LYS cc_start: 0.8623 (mtpp) cc_final: 0.8410 (mmmm) REVERT: B 42 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7991 (mt-10) REVERT: B 54 SER cc_start: 0.8644 (t) cc_final: 0.8441 (m) REVERT: B 177 LYS cc_start: 0.8337 (mtpt) cc_final: 0.8053 (mtmm) REVERT: B 257 MET cc_start: 0.8553 (ttm) cc_final: 0.8265 (mtp) REVERT: B 330 PRO cc_start: 0.8792 (Cg_endo) cc_final: 0.8439 (Cg_exo) REVERT: B 338 ARG cc_start: 0.8083 (mtt180) cc_final: 0.7858 (mtp-110) REVERT: B 345 ARG cc_start: 0.8222 (mmm160) cc_final: 0.7915 (mmm-85) REVERT: B 377 MET cc_start: 0.8835 (mmp) cc_final: 0.8629 (mmt) REVERT: B 398 TYR cc_start: 0.8705 (m-80) cc_final: 0.7362 (m-80) REVERT: B 425 ASP cc_start: 0.8131 (t0) cc_final: 0.7820 (t0) REVERT: C 90 ASN cc_start: 0.8266 (m110) cc_final: 0.8021 (m110) outliers start: 19 outliers final: 9 residues processed: 249 average time/residue: 0.5685 time to fit residues: 149.7216 Evaluate side-chains 249 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 240 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 395 LYS Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 71 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.140479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.129027 restraints weight = 14281.604| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.99 r_work: 0.3565 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9116 Z= 0.149 Angle : 0.642 11.594 12339 Z= 0.327 Chirality : 0.045 0.177 1356 Planarity : 0.005 0.070 1617 Dihedral : 5.275 50.289 1241 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.37 % Allowed : 23.57 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.81 (0.25), residues: 1113 helix: 1.56 (0.27), residues: 376 sheet: 0.91 (0.36), residues: 210 loop : -0.33 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 108 TYR 0.016 0.001 TYR A 320 PHE 0.027 0.001 PHE B 361 TRP 0.003 0.001 TRP A 159 HIS 0.005 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 9114) covalent geometry : angle 0.64151 / 0.33 (12339) hydrogen bonds : bond 0.03783 / 2.47 ( 406) hydrogen bonds : angle 5.05175 / 3.53 ( 1140) Misc. bond : bond 0.00080 / 0.04 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 239 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7659 (mp0) REVERT: A 33 THR cc_start: 0.8027 (t) cc_final: 0.7769 (m) REVERT: A 42 GLU cc_start: 0.7904 (pp20) cc_final: 0.7403 (pp20) REVERT: A 51 ASP cc_start: 0.8216 (t70) cc_final: 0.7841 (t0) REVERT: A 55 ILE cc_start: 0.8745 (mm) cc_final: 0.8438 (mt) REVERT: A 276 SER cc_start: 0.8515 (m) cc_final: 0.8114 (t) REVERT: A 338 ARG cc_start: 0.8081 (mtt180) cc_final: 0.7868 (mtt90) REVERT: A 441 ASP cc_start: 0.8091 (m-30) cc_final: 0.7792 (m-30) REVERT: B 16 LYS cc_start: 0.8621 (mtpp) cc_final: 0.8405 (mmmm) REVERT: B 42 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8001 (mt-10) REVERT: B 54 SER cc_start: 0.8630 (t) cc_final: 0.8420 (m) REVERT: B 177 LYS cc_start: 0.8337 (mtpt) cc_final: 0.8044 (mtmm) REVERT: B 257 MET cc_start: 0.8541 (ttm) cc_final: 0.8253 (mtp) REVERT: B 277 LYS cc_start: 0.8658 (tttt) cc_final: 0.8430 (tttp) REVERT: B 330 PRO cc_start: 0.8808 (Cg_endo) cc_final: 0.8446 (Cg_exo) REVERT: B 338 ARG cc_start: 0.8059 (mtt180) cc_final: 0.7828 (mtp-110) REVERT: B 345 ARG cc_start: 0.8216 (mmm160) cc_final: 0.7926 (mmm-85) REVERT: B 377 MET cc_start: 0.8830 (mmp) cc_final: 0.8620 (mmt) REVERT: B 398 TYR cc_start: 0.8670 (m-80) cc_final: 0.7098 (m-80) REVERT: B 425 ASP cc_start: 0.8119 (t0) cc_final: 0.7835 (t0) REVERT: C 90 ASN cc_start: 0.8250 (m110) cc_final: 0.8012 (m110) outliers start: 13 outliers final: 9 residues processed: 245 average time/residue: 0.6123 time to fit residues: 158.4356 Evaluate side-chains 242 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 233 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 395 LYS Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 51 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 6 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.140228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.128790 restraints weight = 14259.029| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.98 r_work: 0.3563 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9116 Z= 0.158 Angle : 0.646 11.487 12339 Z= 0.330 Chirality : 0.045 0.178 1356 Planarity : 0.005 0.066 1617 Dihedral : 5.246 49.645 1241 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.27 % Allowed : 24.31 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.78 (0.25), residues: 1113 helix: 1.56 (0.27), residues: 377 sheet: 0.87 (0.36), residues: 210 loop : -0.36 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 108 TYR 0.016 0.001 TYR A 320 PHE 0.024 0.001 PHE B 361 TRP 0.003 0.001 TRP B 159 HIS 0.005 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 9114) covalent geometry : angle 0.64582 / 0.33 (12339) hydrogen bonds : bond 0.03832 / 2.50 ( 406) hydrogen bonds : angle 5.06254 / 3.54 ( 1140) Misc. bond : bond 0.00081 / 0.04 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4453.27 seconds wall clock time: 76 minutes 14.68 seconds (4574.68 seconds total)