Starting phenix.real_space_refine on Sat Aug 23 01:10:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v1y_42892/08_2025/8v1y_42892.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v1y_42892/08_2025/8v1y_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_2025/8v1y_42892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v1y_42892/08_2025/8v1y_42892.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v1y_42892/08_2025/8v1y_42892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v1y_42892/08_2025/8v1y_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-2.0-5787/lib/python3.9/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: 2.38, per 1000 atoms: 0.27 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: 0.88 Conformation dependent library (CDL) restraints added in 338.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.37 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: 1.63 Time building geometry restraints manager: 1.14 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 - 2.28: 12208 2.28 - 4.56: 103 4.56 - 6.83: 19 6.83 - 9.11: 3 9.11 - 11.39: 6 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=" C2' AMP B 501 " pdb=" C3' AMP B 501 " pdb=" C4' AMP B 501 " ideal model delta sigma weight residual 111.00 99.61 11.39 3.00e+00 1.11e-01 1.44e+01 angle pdb=" C1' AMP B 501 " pdb=" C2' AMP B 501 " pdb=" C3' AMP B 501 " ideal model delta sigma weight residual 111.00 101.35 9.65 3.00e+00 1.11e-01 1.04e+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 ... (remaining 12334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 5012 17.40 - 34.81: 393 34.81 - 52.21: 50 52.21 - 69.61: 18 69.61 - 87.02: 6 Dihedral angle restraints: 5479 sinusoidal: 2206 harmonic: 3273 Sorted by residual: 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 dihedral pdb=" CA THR A 228 " pdb=" C THR A 228 " pdb=" N MET A 229 " pdb=" CA MET A 229 " ideal model delta harmonic sigma weight residual 180.00 -163.41 -16.59 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 5476 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 850 0.031 - 0.061: 327 0.061 - 0.092: 95 0.092 - 0.122: 73 0.122 - 0.153: 11 Chirality restraints: 1356 Sorted by residual: 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 chirality pdb=" CA PHE A 361 " pdb=" N PHE A 361 " pdb=" C PHE A 361 " pdb=" CB PHE A 361 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.76e-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: 1.600 Set stop_for_unknowns flag: 0.010 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.190 Find NCS groups from input model: 0.160 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:7.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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= 0.184 Angle : 0.555 11.390 12339 Z= 0.260 Chirality : 0.042 0.153 1356 Planarity : 0.004 0.052 1617 Dihedral : 12.778 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 aren 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 covalent geometry : bond 0.00329 ( 9114) covalent geometry : angle 0.55513 (12339) hydrogen bonds : bond 0.17194 ( 406) hydrogen bonds : angle 6.86188 ( 1140) Misc. bond : bond 0.06274 ( 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 : 0.353 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: 0.8341 (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: 0.8647 (m-30) REVERT: B 32 VAL cc_start: 0.8733 (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: 0.6793 time to fit residues: 224.9390 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 : 0.275 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 31 HIS A 212 HIS ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN B 160 ASN D 35 GLN ** D 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.138352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.126634 restraints weight = 14310.294| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.00 r_work: 0.3541 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1861 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= 0.313 Angle : 0.658 7.963 12339 Z= 0.339 Chirality : 0.050 0.207 1356 Planarity : 0.006 0.057 1617 Dihedral : 4.790 45.109 1243 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.69 % Allowed : 13.53 % Favored : 84.78 % 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 aren not related in a simple way. whole: 0.77 (0.25), residues: 1113 helix: 1.24 (0.27), residues: 375 sheet: 1.15 (0.36), residues: 205 loop : -0.22 (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 0.005 0.002 TRP B 159 HIS 0.007 0.001 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.00714 ( 9114) covalent geometry : angle 0.65836 (12339) hydrogen bonds : bond 0.05238 ( 406) hydrogen bonds : angle 5.51377 ( 1140) Misc. bond : bond 0.00155 ( 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 274 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 258 time to evaluate : 0.354 Fit side-chains REVERT: A 2 SER cc_start: 0.7866 (t) cc_final: 0.7606 (p) REVERT: A 4 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7642 (mp0) REVERT: A 12 GLU cc_start: 0.7694 (tt0) cc_final: 0.7427 (tt0) REVERT: A 42 GLU cc_start: 0.7958 (pp20) cc_final: 0.7431 (pp20) REVERT: A 155 ILE cc_start: 0.8509 (mt) cc_final: 0.8263 (tp) REVERT: A 269 MET cc_start: 0.8728 (ttp) cc_final: 0.8433 (ttp) REVERT: A 276 SER cc_start: 0.8600 (m) cc_final: 0.8215 (t) REVERT: B 10 LEU cc_start: 0.8451 (mt) cc_final: 0.8240 (mp) REVERT: B 32 VAL cc_start: 0.8482 (t) cc_final: 0.8276 (p) REVERT: B 42 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7955 (mt-10) REVERT: B 54 SER cc_start: 0.8659 (t) cc_final: 0.8445 (m) REVERT: B 177 LYS cc_start: 0.8488 (mtpt) cc_final: 0.7912 (mtmm) REVERT: B 277 LYS cc_start: 0.8722 (tttt) cc_final: 0.8467 (tttp) REVERT: B 345 ARG cc_start: 0.8226 (mmm160) cc_final: 0.7926 (mmm-85) REVERT: B 377 MET cc_start: 0.8802 (mmp) cc_final: 0.8600 (mmt) REVERT: B 398 TYR cc_start: 0.8818 (m-80) cc_final: 0.7640 (m-80) REVERT: B 425 ASP cc_start: 0.8037 (t0) cc_final: 0.7668 (t0) REVERT: C 90 ASN cc_start: 0.8368 (m110) cc_final: 0.8165 (m110) REVERT: D 65 MET cc_start: 0.7161 (mtt) cc_final: 0.6931 (mtt) outliers start: 16 outliers final: 11 residues processed: 262 average time/residue: 0.6389 time to fit residues: 176.8740 Evaluate side-chains 253 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 242 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 446 LEU Chi-restraints excluded: chain B residue 33 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: 0.5980 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 0.0670 chunk 62 optimal weight: 4.9990 chunk 59 optimal weight: 0.0370 chunk 39 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 95 optimal weight: 0.0060 overall best weight: 0.2412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3872 r_free = 0.3872 target = 0.142243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.130432 restraints weight = 14247.762| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.03 r_work: 0.3590 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9116 Z= 0.111 Angle : 0.567 8.073 12339 Z= 0.285 Chirality : 0.044 0.196 1356 Planarity : 0.005 0.060 1617 Dihedral : 4.510 43.505 1243 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.37 % Allowed : 18.60 % 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 aren not related in a simple way. whole: 0.84 (0.25), residues: 1113 helix: 1.48 (0.27), residues: 375 sheet: 1.13 (0.36), residues: 207 loop : -0.31 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 108 TYR 0.013 0.001 TYR B 239 PHE 0.022 0.001 PHE B 361 TRP 0.003 0.000 TRP A 159 HIS 0.006 0.001 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9114) covalent geometry : angle 0.56718 (12339) hydrogen bonds : bond 0.03771 ( 406) hydrogen bonds : angle 5.05043 ( 1140) Misc. bond : bond 0.00054 ( 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 269 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 256 time to evaluate : 0.345 Fit side-chains REVERT: A 2 SER cc_start: 0.7806 (t) cc_final: 0.7499 (p) REVERT: A 4 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7607 (mp0) REVERT: A 12 GLU cc_start: 0.7611 (tt0) cc_final: 0.7365 (tt0) REVERT: A 33 THR cc_start: 0.7965 (t) cc_final: 0.7696 (m) REVERT: A 42 GLU cc_start: 0.7875 (pp20) cc_final: 0.7401 (pp20) REVERT: A 55 ILE cc_start: 0.8691 (mm) cc_final: 0.8361 (mt) REVERT: A 155 ILE cc_start: 0.8509 (mt) cc_final: 0.8285 (tp) REVERT: A 269 MET cc_start: 0.8734 (ttp) cc_final: 0.8427 (ttp) REVERT: A 276 SER cc_start: 0.8534 (m) cc_final: 0.8140 (t) REVERT: A 338 ARG cc_start: 0.8084 (mtt180) cc_final: 0.7808 (mtt90) REVERT: A 441 ASP cc_start: 0.8172 (m-30) cc_final: 0.7793 (m-30) REVERT: B 10 LEU cc_start: 0.8446 (mt) cc_final: 0.8237 (mp) REVERT: B 42 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7941 (mt-10) REVERT: B 49 MET cc_start: 0.8585 (mtp) cc_final: 0.8369 (mmm) REVERT: B 110 LYS cc_start: 0.8542 (mttp) cc_final: 0.8330 (mttt) REVERT: B 137 ASP cc_start: 0.8040 (m-30) cc_final: 0.7778 (m-30) REVERT: B 177 LYS cc_start: 0.8370 (mtpt) cc_final: 0.7824 (mtmm) REVERT: B 224 THR cc_start: 0.8572 (m) cc_final: 0.8152 (p) REVERT: B 277 LYS cc_start: 0.8672 (tttt) cc_final: 0.8335 (tttp) REVERT: B 332 MET cc_start: 0.8088 (mmm) cc_final: 0.7862 (ttp) REVERT: B 338 ARG cc_start: 0.8076 (mtt180) cc_final: 0.7844 (mtp-110) REVERT: B 345 ARG cc_start: 0.8212 (mmm160) cc_final: 0.7931 (mmm-85) REVERT: B 398 TYR cc_start: 0.8731 (m-80) cc_final: 0.7464 (m-80) REVERT: B 425 ASP cc_start: 0.8077 (t0) cc_final: 0.7745 (t0) REVERT: B 438 GLU cc_start: 0.8010 (mp0) cc_final: 0.7797 (mp0) REVERT: B 461 VAL cc_start: 0.8776 (t) cc_final: 0.8574 (m) REVERT: D 76 GLU cc_start: 0.8153 (tp30) cc_final: 0.7940 (tp30) REVERT: D 102 MET cc_start: 0.8028 (ttp) cc_final: 0.7791 (mtp) outliers start: 13 outliers final: 9 residues processed: 259 average time/residue: 0.6196 time to fit residues: 169.9455 Evaluate side-chains 258 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 249 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ASN 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: 4.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 GLN C 90 ASN C 116 HIS ** D 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.139543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.127828 restraints weight = 14337.068| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.02 r_work: 0.3552 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9116 Z= 0.208 Angle : 0.611 8.788 12339 Z= 0.308 Chirality : 0.046 0.198 1356 Planarity : 0.005 0.062 1617 Dihedral : 4.604 44.585 1243 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.64 % Allowed : 19.34 % Favored : 78.01 % 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 aren not related in a simple way. whole: 0.78 (0.25), residues: 1113 helix: 1.45 (0.27), residues: 377 sheet: 1.08 (0.37), residues: 205 loop : -0.35 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 108 TYR 0.016 0.001 TYR B 239 PHE 0.029 0.002 PHE A 361 TRP 0.004 0.001 TRP A 159 HIS 0.006 0.001 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 9114) covalent geometry : angle 0.61070 (12339) hydrogen bonds : bond 0.04209 ( 406) hydrogen bonds : angle 5.09582 ( 1140) Misc. bond : bond 0.00129 ( 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 277 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 252 time to evaluate : 0.379 Fit side-chains REVERT: A 2 SER cc_start: 0.7813 (t) cc_final: 0.7548 (p) REVERT: A 4 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7572 (mt-10) REVERT: A 12 GLU cc_start: 0.7683 (tt0) cc_final: 0.7419 (tt0) REVERT: A 33 THR cc_start: 0.8035 (t) cc_final: 0.7775 (m) REVERT: A 42 GLU cc_start: 0.7914 (pp20) cc_final: 0.7382 (pp20) REVERT: A 154 ASP cc_start: 0.7719 (p0) cc_final: 0.7389 (t70) REVERT: A 155 ILE cc_start: 0.8515 (mt) cc_final: 0.8106 (tp) REVERT: A 276 SER cc_start: 0.8578 (m) cc_final: 0.8169 (t) REVERT: A 338 ARG cc_start: 0.8088 (mtt180) cc_final: 0.7818 (mtt90) REVERT: B 10 LEU cc_start: 0.8477 (mt) cc_final: 0.8264 (mp) REVERT: B 42 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7979 (mt-10) REVERT: B 177 LYS cc_start: 0.8391 (mtpt) cc_final: 0.7884 (mtmm) REVERT: B 277 LYS cc_start: 0.8663 (tttt) cc_final: 0.8410 (tttp) REVERT: B 338 ARG cc_start: 0.8102 (mtt180) cc_final: 0.7869 (mtp-110) REVERT: B 345 ARG cc_start: 0.8241 (mmm160) cc_final: 0.7965 (mmm-85) REVERT: B 398 TYR cc_start: 0.8732 (m-80) cc_final: 0.7358 (m-80) REVERT: B 425 ASP cc_start: 0.8065 (t0) cc_final: 0.7709 (t0) REVERT: B 429 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7818 (pt) outliers start: 25 outliers final: 17 residues processed: 260 average time/residue: 0.6746 time to fit residues: 185.3673 Evaluate side-chains 265 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 247 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 A residue 416 GLU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 97 THR 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 Chi-restraints excluded: chain D residue 101 ASN 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: 2.9990 chunk 82 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 95 optimal weight: 0.0980 chunk 109 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN C 90 ASN D 35 GLN ** D 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.140261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.128831 restraints weight = 14371.200| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.99 r_work: 0.3571 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9116 Z= 0.135 Angle : 0.592 8.882 12339 Z= 0.298 Chirality : 0.045 0.193 1356 Planarity : 0.005 0.064 1617 Dihedral : 4.534 45.608 1243 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.33 % Allowed : 20.61 % Favored : 77.06 % 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 aren not related in a simple way. whole: 0.84 (0.25), residues: 1113 helix: 1.59 (0.27), residues: 376 sheet: 1.04 (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 C 108 TYR 0.014 0.001 TYR B 239 PHE 0.027 0.001 PHE A 361 TRP 0.004 0.001 TRP A 159 HIS 0.004 0.001 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9114) covalent geometry : angle 0.59195 (12339) hydrogen bonds : bond 0.03755 ( 406) hydrogen bonds : angle 4.95580 ( 1140) Misc. bond : bond 0.00080 ( 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 268 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 246 time to evaluate : 0.365 Fit side-chains REVERT: A 12 GLU cc_start: 0.7682 (tt0) cc_final: 0.7406 (tt0) REVERT: A 33 THR cc_start: 0.7998 (t) cc_final: 0.7726 (m) REVERT: A 42 GLU cc_start: 0.7879 (pp20) cc_final: 0.7353 (pp20) REVERT: A 55 ILE cc_start: 0.8708 (mm) cc_final: 0.8388 (mt) REVERT: A 154 ASP cc_start: 0.7654 (p0) cc_final: 0.7371 (t70) REVERT: A 155 ILE cc_start: 0.8508 (mt) cc_final: 0.8043 (tp) REVERT: A 276 SER cc_start: 0.8553 (m) cc_final: 0.8131 (t) REVERT: A 338 ARG cc_start: 0.8082 (mtt180) cc_final: 0.7842 (mtt90) REVERT: A 441 ASP cc_start: 0.8149 (m-30) cc_final: 0.7824 (m-30) REVERT: B 16 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8466 (mmmm) REVERT: B 42 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7999 (mt-10) REVERT: B 177 LYS cc_start: 0.8340 (mtpt) cc_final: 0.8054 (mtmm) REVERT: B 257 MET cc_start: 0.8518 (ttm) cc_final: 0.8268 (mtp) REVERT: B 277 LYS cc_start: 0.8611 (tttt) cc_final: 0.8383 (tttp) REVERT: B 338 ARG cc_start: 0.8094 (mtt180) cc_final: 0.7851 (mtp-110) REVERT: B 345 ARG cc_start: 0.8253 (mmm160) cc_final: 0.7957 (mmm-85) REVERT: B 398 TYR cc_start: 0.8716 (m-80) cc_final: 0.7444 (m-80) REVERT: B 425 ASP cc_start: 0.8122 (t0) cc_final: 0.7758 (t0) outliers start: 22 outliers final: 13 residues processed: 254 average time/residue: 0.6343 time to fit residues: 170.2550 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 : 0.331 ------------------------------------------------------------------------------- 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 416 GLU Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 73 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 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 Chi-restraints excluded: chain D residue 101 ASN 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: 1.9990 chunk 6 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3830 r_free = 0.3830 target = 0.138356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.126724 restraints weight = 14395.726| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.01 r_work: 0.3544 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 9116 Z= 0.204 Angle : 0.620 9.224 12339 Z= 0.315 Chirality : 0.046 0.201 1356 Planarity : 0.006 0.066 1617 Dihedral : 4.641 47.480 1243 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.33 % Allowed : 20.93 % Favored : 76.74 % 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 aren not related in a simple way. whole: 0.74 (0.25), residues: 1113 helix: 1.51 (0.27), residues: 377 sheet: 1.00 (0.37), residues: 205 loop : -0.43 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 108 TYR 0.016 0.001 TYR B 239 PHE 0.026 0.002 PHE A 361 TRP 0.004 0.001 TRP B 159 HIS 0.005 0.001 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 9114) covalent geometry : angle 0.61986 (12339) hydrogen bonds : bond 0.04085 ( 406) hydrogen bonds : angle 5.10292 ( 1140) Misc. bond : bond 0.00109 ( 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 274 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 252 time to evaluate : 0.214 Fit side-chains REVERT: A 12 GLU cc_start: 0.7655 (tt0) cc_final: 0.7384 (tt0) REVERT: A 33 THR cc_start: 0.8050 (t) cc_final: 0.7785 (m) REVERT: A 42 GLU cc_start: 0.7887 (pp20) cc_final: 0.7375 (pp20) REVERT: A 55 ILE cc_start: 0.8722 (mm) cc_final: 0.8418 (mt) REVERT: A 154 ASP cc_start: 0.7737 (p0) cc_final: 0.7501 (t70) REVERT: A 155 ILE cc_start: 0.8552 (mt) cc_final: 0.8110 (tp) REVERT: A 200 MET cc_start: 0.8640 (mtt) cc_final: 0.8412 (mtt) REVERT: A 276 SER cc_start: 0.8587 (m) cc_final: 0.8143 (t) REVERT: A 338 ARG cc_start: 0.8003 (mtt180) cc_final: 0.7773 (mtt90) REVERT: A 441 ASP cc_start: 0.8158 (m-30) cc_final: 0.7844 (m-30) REVERT: B 16 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8456 (mmmm) REVERT: B 42 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8078 (mt-10) REVERT: B 177 LYS cc_start: 0.8330 (mtpt) cc_final: 0.8043 (mtmm) REVERT: B 277 LYS cc_start: 0.8633 (tttt) cc_final: 0.8420 (tttp) REVERT: B 330 PRO cc_start: 0.8750 (Cg_endo) cc_final: 0.8401 (Cg_exo) REVERT: B 338 ARG cc_start: 0.8095 (mtt180) cc_final: 0.7868 (mtp-110) REVERT: B 345 ARG cc_start: 0.8219 (mmm160) cc_final: 0.7939 (mmm-85) REVERT: B 398 TYR cc_start: 0.8672 (m-80) cc_final: 0.7398 (m-80) REVERT: B 425 ASP cc_start: 0.8104 (t0) cc_final: 0.7732 (t0) REVERT: C 38 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8596 (p) outliers start: 22 outliers final: 14 residues processed: 258 average time/residue: 0.6818 time to fit residues: 185.1444 Evaluate side-chains 261 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 245 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 HIS Chi-restraints excluded: chain A residue 257 MET 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 54 SER 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 C residue 62 LEU Chi-restraints excluded: chain D residue 50 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 96 optimal weight: 3.9990 chunk 15 optimal weight: 0.0470 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 41 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN ** 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 = 0.3849 r_free = 0.3849 target = 0.139764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.128172 restraints weight = 14411.614| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.02 r_work: 0.3574 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9116 Z= 0.140 Angle : 0.606 8.993 12339 Z= 0.308 Chirality : 0.045 0.187 1356 Planarity : 0.005 0.066 1617 Dihedral : 4.572 47.423 1243 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.71 % Favored : 98.20 % Rotamer: Outliers : 2.11 % Allowed : 21.88 % Favored : 76.00 % 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 aren not related in a simple way. whole: 0.75 (0.25), residues: 1113 helix: 1.54 (0.27), residues: 381 sheet: 0.93 (0.37), residues: 209 loop : -0.43 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 108 TYR 0.014 0.001 TYR B 239 PHE 0.024 0.001 PHE A 361 TRP 0.003 0.001 TRP A 159 HIS 0.005 0.001 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9114) covalent geometry : angle 0.60613 (12339) hydrogen bonds : bond 0.03724 ( 406) hydrogen bonds : angle 5.00338 ( 1140) Misc. bond : bond 0.00079 ( 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 265 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 245 time to evaluate : 0.268 Fit side-chains REVERT: A 12 GLU cc_start: 0.7652 (tt0) cc_final: 0.7393 (tt0) REVERT: A 33 THR cc_start: 0.8007 (t) cc_final: 0.7732 (m) REVERT: A 42 GLU cc_start: 0.7867 (pp20) cc_final: 0.7349 (pp20) REVERT: A 55 ILE cc_start: 0.8718 (mm) cc_final: 0.8415 (mt) REVERT: A 154 ASP cc_start: 0.7665 (p0) cc_final: 0.7415 (t70) REVERT: A 155 ILE cc_start: 0.8535 (mt) cc_final: 0.8077 (tp) REVERT: A 200 MET cc_start: 0.8642 (mtt) cc_final: 0.8394 (mtt) REVERT: A 276 SER cc_start: 0.8570 (m) cc_final: 0.8117 (t) REVERT: A 338 ARG cc_start: 0.7998 (mtt180) cc_final: 0.7790 (mtt90) REVERT: A 441 ASP cc_start: 0.8100 (m-30) cc_final: 0.7801 (m-30) REVERT: B 16 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8445 (mmmm) REVERT: B 42 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8070 (mt-10) REVERT: B 177 LYS cc_start: 0.8306 (mtpt) cc_final: 0.8012 (mtmm) REVERT: B 277 LYS cc_start: 0.8648 (tttt) cc_final: 0.8441 (tttp) REVERT: B 330 PRO cc_start: 0.8746 (Cg_endo) cc_final: 0.8395 (Cg_exo) REVERT: B 338 ARG cc_start: 0.8040 (mtt180) cc_final: 0.7809 (mtp-110) REVERT: B 345 ARG cc_start: 0.8205 (mmm160) cc_final: 0.7926 (mmm-85) REVERT: B 398 TYR cc_start: 0.8672 (m-80) cc_final: 0.7448 (m-80) REVERT: B 425 ASP cc_start: 0.8111 (t0) cc_final: 0.7786 (t0) REVERT: C 38 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8592 (p) outliers start: 20 outliers final: 13 residues processed: 252 average time/residue: 0.6165 time to fit residues: 163.8529 Evaluate side-chains 262 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 247 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 HIS Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 416 GLU 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 265 ASN 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 10 ILE Chi-restraints excluded: chain D residue 50 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 87 optimal weight: 3.9990 chunk 84 optimal weight: 0.0470 chunk 18 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** 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 = 0.3820 r_free = 0.3820 target = 0.137592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.125938 restraints weight = 14282.215| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.01 r_work: 0.3541 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9116 Z= 0.258 Angle : 0.669 9.583 12339 Z= 0.340 Chirality : 0.048 0.217 1356 Planarity : 0.006 0.070 1617 Dihedral : 4.845 50.448 1243 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.43 % Allowed : 21.14 % Favored : 76.43 % 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 aren not related in a simple way. whole: 0.56 (0.25), residues: 1113 helix: 1.35 (0.27), residues: 381 sheet: 0.92 (0.37), residues: 205 loop : -0.56 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 108 TYR 0.018 0.002 TYR B 239 PHE 0.027 0.002 PHE A 361 TRP 0.005 0.001 TRP B 159 HIS 0.005 0.001 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00594 ( 9114) covalent geometry : angle 0.66860 (12339) hydrogen bonds : bond 0.04412 ( 406) hydrogen bonds : angle 5.23016 ( 1140) Misc. bond : bond 0.00146 ( 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 269 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 246 time to evaluate : 0.347 Fit side-chains REVERT: A 12 GLU cc_start: 0.7699 (tt0) cc_final: 0.7422 (tt0) REVERT: A 42 GLU cc_start: 0.7896 (pp20) cc_final: 0.7407 (pp20) REVERT: A 55 ILE cc_start: 0.8739 (mm) cc_final: 0.8446 (mt) REVERT: A 155 ILE cc_start: 0.8546 (mt) cc_final: 0.8106 (tp) REVERT: A 276 SER cc_start: 0.8604 (m) cc_final: 0.8165 (t) REVERT: A 338 ARG cc_start: 0.8045 (mtt180) cc_final: 0.7825 (mtt90) REVERT: B 16 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8475 (mmmm) REVERT: B 42 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8072 (mt-10) REVERT: B 177 LYS cc_start: 0.8378 (mtpt) cc_final: 0.8092 (mtmm) REVERT: B 330 PRO cc_start: 0.8771 (Cg_endo) cc_final: 0.8430 (Cg_exo) REVERT: B 338 ARG cc_start: 0.8142 (mtt180) cc_final: 0.7923 (mtp-110) REVERT: B 345 ARG cc_start: 0.8185 (mmm160) cc_final: 0.7928 (mmm-85) REVERT: B 398 TYR cc_start: 0.8679 (m-80) cc_final: 0.7374 (m-80) REVERT: B 425 ASP cc_start: 0.8127 (t0) cc_final: 0.7730 (t0) REVERT: C 38 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8582 (p) outliers start: 23 outliers final: 12 residues processed: 253 average time/residue: 0.7078 time to fit residues: 188.6419 Evaluate side-chains 256 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 242 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 97 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 293 GLU 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 D residue 33 SER Chi-restraints excluded: chain D residue 50 THR 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: 0.6980 chunk 65 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 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 = 0.3839 r_free = 0.3839 target = 0.139231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.127557 restraints weight = 14178.820| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.01 r_work: 0.3559 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9116 Z= 0.171 Angle : 0.648 10.909 12339 Z= 0.328 Chirality : 0.046 0.197 1356 Planarity : 0.006 0.070 1617 Dihedral : 4.771 50.172 1243 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.22 % Allowed : 22.52 % Favored : 75.26 % 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 aren not related in a simple way. whole: 0.70 (0.25), residues: 1113 helix: 1.53 (0.27), residues: 377 sheet: 0.91 (0.37), residues: 203 loop : -0.47 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 108 TYR 0.015 0.001 TYR A 320 PHE 0.025 0.001 PHE A 361 TRP 0.004 0.001 TRP A 159 HIS 0.004 0.001 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 9114) covalent geometry : angle 0.64849 (12339) hydrogen bonds : bond 0.03955 ( 406) hydrogen bonds : angle 5.10738 ( 1140) Misc. bond : bond 0.00097 ( 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 264 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 243 time to evaluate : 0.379 Fit side-chains REVERT: A 12 GLU cc_start: 0.7636 (tt0) cc_final: 0.7364 (tt0) REVERT: A 33 THR cc_start: 0.8030 (t) cc_final: 0.7769 (m) REVERT: A 42 GLU cc_start: 0.7867 (pp20) cc_final: 0.7374 (pp20) REVERT: A 55 ILE cc_start: 0.8744 (mm) cc_final: 0.8447 (mt) REVERT: A 276 SER cc_start: 0.8583 (m) cc_final: 0.8136 (t) REVERT: A 338 ARG cc_start: 0.8004 (mtt180) cc_final: 0.7786 (mtt90) REVERT: A 441 ASP cc_start: 0.8147 (m-30) cc_final: 0.7825 (m-30) REVERT: B 16 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8457 (mmmm) REVERT: B 42 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8058 (mt-10) REVERT: B 177 LYS cc_start: 0.8321 (mtpt) cc_final: 0.8037 (mtmm) REVERT: B 225 ARG cc_start: 0.8200 (ttp80) cc_final: 0.7792 (ttp80) REVERT: B 330 PRO cc_start: 0.8745 (Cg_endo) cc_final: 0.8405 (Cg_exo) REVERT: B 338 ARG cc_start: 0.8092 (mtt180) cc_final: 0.7871 (mtp-110) REVERT: B 345 ARG cc_start: 0.8208 (mmm160) cc_final: 0.7932 (mmm-85) REVERT: B 398 TYR cc_start: 0.8627 (m-80) cc_final: 0.7309 (m-80) REVERT: B 425 ASP cc_start: 0.8142 (t0) cc_final: 0.7794 (t0) REVERT: C 38 THR cc_start: 0.8799 (OUTLIER) cc_final: 0.8581 (p) outliers start: 21 outliers final: 13 residues processed: 250 average time/residue: 0.6814 time to fit residues: 179.6938 Evaluate side-chains 259 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 244 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 33 THR 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 D residue 33 SER Chi-restraints excluded: chain D residue 50 THR 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: 1.9990 chunk 31 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 96 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.140088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.128428 restraints weight = 14214.089| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.01 r_work: 0.3570 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9116 Z= 0.143 Angle : 0.639 11.547 12339 Z= 0.323 Chirality : 0.045 0.180 1356 Planarity : 0.006 0.073 1617 Dihedral : 4.735 49.177 1243 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.69 % Allowed : 23.26 % 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 aren not related in a simple way. whole: 0.80 (0.25), residues: 1113 helix: 1.61 (0.27), residues: 376 sheet: 0.90 (0.37), residues: 208 loop : -0.38 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 108 TYR 0.015 0.001 TYR A 320 PHE 0.023 0.001 PHE A 361 TRP 0.003 0.001 TRP A 159 HIS 0.005 0.001 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9114) covalent geometry : angle 0.63922 (12339) hydrogen bonds : bond 0.03770 ( 406) hydrogen bonds : angle 5.04954 ( 1140) Misc. bond : bond 0.00111 ( 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 256 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 240 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 12 GLU cc_start: 0.7607 (tt0) cc_final: 0.7353 (tt0) REVERT: A 33 THR cc_start: 0.8023 (t) cc_final: 0.7767 (m) REVERT: A 42 GLU cc_start: 0.7866 (pp20) cc_final: 0.7370 (pp20) REVERT: A 55 ILE cc_start: 0.8733 (mm) cc_final: 0.8433 (mt) REVERT: A 276 SER cc_start: 0.8571 (m) cc_final: 0.8116 (t) REVERT: A 338 ARG cc_start: 0.8006 (mtt180) cc_final: 0.7799 (mtt90) REVERT: A 441 ASP cc_start: 0.8145 (m-30) cc_final: 0.7828 (m-30) REVERT: B 16 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8452 (mmmm) REVERT: B 42 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8059 (mt-10) REVERT: B 177 LYS cc_start: 0.8310 (mtpt) cc_final: 0.8019 (mtmm) REVERT: B 330 PRO cc_start: 0.8757 (Cg_endo) cc_final: 0.8406 (Cg_exo) REVERT: B 338 ARG cc_start: 0.8096 (mtt180) cc_final: 0.7868 (mtp-110) REVERT: B 345 ARG cc_start: 0.8215 (mmm160) cc_final: 0.7930 (mmm-85) REVERT: B 398 TYR cc_start: 0.8661 (m-80) cc_final: 0.7413 (m-80) REVERT: B 425 ASP cc_start: 0.8144 (t0) cc_final: 0.7794 (t0) REVERT: C 38 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8570 (p) outliers start: 16 outliers final: 13 residues processed: 245 average time/residue: 0.6898 time to fit residues: 178.1781 Evaluate side-chains 256 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 241 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 397 LEU 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 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 50 THR 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 6 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 17 optimal weight: 0.0980 chunk 111 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** 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 = 0.3849 r_free = 0.3849 target = 0.140083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.128368 restraints weight = 14272.250| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.02 r_work: 0.3570 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9116 Z= 0.148 Angle : 0.654 11.573 12339 Z= 0.328 Chirality : 0.045 0.184 1356 Planarity : 0.006 0.069 1617 Dihedral : 4.718 49.558 1243 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.90 % Allowed : 23.26 % Favored : 74.84 % 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 aren not related in a simple way. whole: 0.75 (0.25), residues: 1113 helix: 1.58 (0.27), residues: 378 sheet: 0.86 (0.37), residues: 206 loop : -0.42 (0.26), residues: 529 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 0.023 0.001 PHE A 361 TRP 0.003 0.001 TRP A 159 HIS 0.008 0.001 HIS D 103 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 9114) covalent geometry : angle 0.65370 (12339) hydrogen bonds : bond 0.03762 ( 406) hydrogen bonds : angle 5.04728 ( 1140) Misc. bond : bond 0.00091 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4803.20 seconds wall clock time: 82 minutes 14.21 seconds (4934.21 seconds total)