Starting phenix.real_space_refine on Sat Jul 26 22:49:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v1y_42892/07_2025/8v1y_42892.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v1y_42892/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8v1y_42892/07_2025/8v1y_42892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v1y_42892/07_2025/8v1y_42892.map" model { file = "/net/cci-nas-00/data/ceres_data/8v1y_42892/07_2025/8v1y_42892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v1y_42892/07_2025/8v1y_42892.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 10.29, per 1000 atoms: 1.15 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: 3.45 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.32 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: 3.78 Time building geometry restraints manager: 3.82 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 469 or resid 501)) selection = (chain 'B' and (resid 1 through 59 or resid 62 through 469 or resid 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: 4.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 33.960 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:16.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.820 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.001 0.000 TRP B 58 HIS 0.003 0.000 HIS B 210 PHE 0.016 0.001 PHE B 361 TYR 0.011 0.001 TYR B 239 ARG 0.002 0.000 ARG A 103 Details of bonding type rmsd hydrogen bonds : bond 0.17194 ( 406) hydrogen bonds : angle 6.86188 ( 1140) covalent geometry : bond 0.00329 ( 9114) covalent geometry : angle 0.55513 (12339) 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 : 0.975 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: 1.3974 time to fit residues: 463.8529 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 : 1.076 ------------------------------------------------------------------------------- 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 94 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3843 r_free = 0.3843 target = 0.139819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.128077 restraints weight = 14136.130| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.99 r_work: 0.3562 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9116 Z= 0.219 Angle : 0.614 7.727 12339 Z= 0.314 Chirality : 0.047 0.190 1356 Planarity : 0.006 0.054 1617 Dihedral : 4.631 42.672 1243 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.59 % Allowed : 13.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.25), residues: 1113 helix: 1.38 (0.27), residues: 376 sheet: 1.19 (0.36), residues: 204 loop : -0.21 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 159 HIS 0.004 0.001 HIS D 92 PHE 0.021 0.002 PHE B 361 TYR 0.016 0.002 TYR B 239 ARG 0.008 0.001 ARG C 108 Details of bonding type rmsd hydrogen bonds : bond 0.04709 ( 406) hydrogen bonds : angle 5.34873 ( 1140) covalent geometry : bond 0.00500 ( 9114) covalent geometry : angle 0.61439 (12339) Misc. bond : bond 0.00126 ( 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: 15 poor density : 260 time to evaluate : 0.987 Fit side-chains REVERT: A 2 SER cc_start: 0.7840 (t) cc_final: 0.7581 (p) REVERT: A 4 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7633 (mp0) REVERT: A 12 GLU cc_start: 0.7632 (tt0) cc_final: 0.7381 (tt0) REVERT: A 33 THR cc_start: 0.8071 (t) cc_final: 0.7811 (m) REVERT: A 42 GLU cc_start: 0.7934 (pp20) cc_final: 0.7382 (pp20) REVERT: A 155 ILE cc_start: 0.8498 (mt) cc_final: 0.8270 (tp) REVERT: A 269 MET cc_start: 0.8723 (ttp) cc_final: 0.8408 (ttp) REVERT: A 276 SER cc_start: 0.8573 (m) cc_final: 0.8186 (t) REVERT: A 357 ILE cc_start: 0.8575 (mp) cc_final: 0.8359 (pt) REVERT: B 32 VAL cc_start: 0.8446 (t) cc_final: 0.8244 (p) REVERT: B 42 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7948 (mt-10) REVERT: B 177 LYS cc_start: 0.8432 (mtpt) cc_final: 0.7872 (mtmm) REVERT: B 277 LYS cc_start: 0.8697 (tttt) cc_final: 0.8425 (tttp) REVERT: B 332 MET cc_start: 0.8064 (mmm) cc_final: 0.7807 (ttp) REVERT: B 345 ARG cc_start: 0.8243 (mmm160) cc_final: 0.7932 (mmm-85) REVERT: B 398 TYR cc_start: 0.8822 (m-80) cc_final: 0.7563 (m-80) REVERT: B 425 ASP cc_start: 0.8032 (t0) cc_final: 0.7690 (t0) REVERT: C 90 ASN cc_start: 0.8331 (m110) cc_final: 0.8116 (m110) REVERT: D 35 GLN cc_start: 0.7713 (tm-30) cc_final: 0.7483 (tp-100) REVERT: D 65 MET cc_start: 0.7096 (mtt) cc_final: 0.6874 (mtt) REVERT: D 102 MET cc_start: 0.8138 (ttp) cc_final: 0.7779 (mtp) outliers start: 15 outliers final: 11 residues processed: 263 average time/residue: 1.3077 time to fit residues: 364.1122 Evaluate side-chains 261 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 250 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 49 MET 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 58 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 2 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 95 optimal weight: 0.0970 chunk 3 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 116 HIS ** D 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.139641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.127812 restraints weight = 14330.082| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.04 r_work: 0.3552 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9116 Z= 0.201 Angle : 0.603 8.653 12339 Z= 0.304 Chirality : 0.047 0.211 1356 Planarity : 0.005 0.061 1617 Dihedral : 4.632 46.690 1243 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.22 % Allowed : 18.39 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.25), residues: 1113 helix: 1.34 (0.27), residues: 375 sheet: 1.15 (0.37), residues: 205 loop : -0.26 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 159 HIS 0.006 0.001 HIS C 116 PHE 0.031 0.002 PHE A 361 TYR 0.016 0.001 TYR B 239 ARG 0.006 0.001 ARG C 108 Details of bonding type rmsd hydrogen bonds : bond 0.04341 ( 406) hydrogen bonds : angle 5.19544 ( 1140) covalent geometry : bond 0.00461 ( 9114) covalent geometry : angle 0.60298 (12339) Misc. bond : bond 0.00125 ( 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 279 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 258 time to evaluate : 0.958 Fit side-chains REVERT: A 2 SER cc_start: 0.7829 (t) cc_final: 0.7521 (p) REVERT: A 4 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7623 (mp0) REVERT: A 12 GLU cc_start: 0.7693 (tt0) cc_final: 0.7435 (tt0) REVERT: A 33 THR cc_start: 0.8040 (t) cc_final: 0.7774 (m) REVERT: A 42 GLU cc_start: 0.7919 (pp20) cc_final: 0.7392 (pp20) REVERT: A 154 ASP cc_start: 0.7707 (p0) cc_final: 0.7456 (t70) REVERT: A 155 ILE cc_start: 0.8564 (mt) cc_final: 0.8104 (tp) REVERT: A 276 SER cc_start: 0.8593 (m) cc_final: 0.8195 (t) REVERT: A 338 ARG cc_start: 0.8101 (mtt180) cc_final: 0.7828 (mtt90) REVERT: A 357 ILE cc_start: 0.8605 (mp) cc_final: 0.8399 (pt) REVERT: B 42 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7954 (mt-10) REVERT: B 54 SER cc_start: 0.8666 (t) cc_final: 0.8451 (m) REVERT: B 177 LYS cc_start: 0.8427 (mtpt) cc_final: 0.7877 (mtmm) REVERT: B 277 LYS cc_start: 0.8687 (tttt) cc_final: 0.8419 (tttp) REVERT: B 338 ARG cc_start: 0.8107 (mtt180) cc_final: 0.7883 (mtp-110) REVERT: B 345 ARG cc_start: 0.8223 (mmm160) cc_final: 0.7939 (mmm-85) REVERT: B 398 TYR cc_start: 0.8761 (m-80) cc_final: 0.7670 (m-80) REVERT: B 425 ASP cc_start: 0.8080 (t0) cc_final: 0.7713 (t0) REVERT: B 438 GLU cc_start: 0.8066 (mp0) cc_final: 0.7651 (mp0) REVERT: C 90 ASN cc_start: 0.8366 (m110) cc_final: 0.8156 (m110) REVERT: D 76 GLU cc_start: 0.8199 (tp30) cc_final: 0.7958 (tp30) outliers start: 21 outliers final: 14 residues processed: 263 average time/residue: 1.3553 time to fit residues: 377.7895 Evaluate side-chains 263 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 249 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 33 THR 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 48 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 108 optimal weight: 0.0970 chunk 77 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 116 HIS D 35 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 = 0.3856 r_free = 0.3856 target = 0.140892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.129202 restraints weight = 14261.174| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.02 r_work: 0.3573 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2325 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= 0.146 Angle : 0.585 8.813 12339 Z= 0.295 Chirality : 0.045 0.193 1356 Planarity : 0.005 0.064 1617 Dihedral : 4.542 46.611 1243 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.43 % Allowed : 19.03 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.25), residues: 1113 helix: 1.48 (0.27), residues: 375 sheet: 1.11 (0.37), residues: 205 loop : -0.30 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 159 HIS 0.005 0.001 HIS C 116 PHE 0.026 0.001 PHE A 361 TYR 0.014 0.001 TYR B 239 ARG 0.006 0.001 ARG A 225 Details of bonding type rmsd hydrogen bonds : bond 0.03856 ( 406) hydrogen bonds : angle 5.03827 ( 1140) covalent geometry : bond 0.00334 ( 9114) covalent geometry : angle 0.58523 (12339) Misc. bond : bond 0.00092 ( 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: 23 poor density : 254 time to evaluate : 1.456 Fit side-chains REVERT: A 4 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7600 (mp0) REVERT: A 12 GLU cc_start: 0.7665 (tt0) cc_final: 0.7408 (tt0) REVERT: A 33 THR cc_start: 0.8027 (t) cc_final: 0.7757 (m) REVERT: A 42 GLU cc_start: 0.7877 (pp20) cc_final: 0.7355 (pp20) REVERT: A 51 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7845 (t0) REVERT: A 55 ILE cc_start: 0.8707 (mm) cc_final: 0.8385 (mt) REVERT: A 155 ILE cc_start: 0.8562 (mt) cc_final: 0.8112 (tp) REVERT: A 276 SER cc_start: 0.8558 (m) cc_final: 0.8153 (t) REVERT: A 338 ARG cc_start: 0.8080 (mtt180) cc_final: 0.7827 (mtt90) REVERT: A 441 ASP cc_start: 0.8169 (m-30) cc_final: 0.7804 (m-30) REVERT: B 42 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7962 (mt-10) REVERT: B 177 LYS cc_start: 0.8375 (mtpt) cc_final: 0.8087 (mtmm) REVERT: B 277 LYS cc_start: 0.8688 (tttt) cc_final: 0.8433 (tttp) REVERT: B 332 MET cc_start: 0.8121 (mmm) cc_final: 0.7883 (tpp) REVERT: B 338 ARG cc_start: 0.8103 (mtt180) cc_final: 0.7877 (mtp-110) REVERT: B 345 ARG cc_start: 0.8234 (mmm160) cc_final: 0.7958 (mmm-85) REVERT: B 398 TYR cc_start: 0.8739 (m-80) cc_final: 0.7553 (m-80) REVERT: B 425 ASP cc_start: 0.8079 (t0) cc_final: 0.7728 (t0) REVERT: B 438 GLU cc_start: 0.8016 (mp0) cc_final: 0.7626 (mp0) REVERT: C 90 ASN cc_start: 0.8347 (m110) cc_final: 0.8128 (m110) REVERT: D 102 MET cc_start: 0.8049 (ttp) cc_final: 0.7842 (mtp) outliers start: 23 outliers final: 14 residues processed: 256 average time/residue: 1.9043 time to fit residues: 514.7354 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 : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP 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 54 SER Chi-restraints excluded: chain B residue 138 ASP 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 87 MET Chi-restraints excluded: chain D residue 50 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 36 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 59 optimal weight: 0.0970 chunk 5 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 116 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.140106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.128663 restraints weight = 14186.480| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 1.98 r_work: 0.3563 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2465 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= 0.145 Angle : 0.588 9.004 12339 Z= 0.295 Chirality : 0.045 0.194 1356 Planarity : 0.005 0.064 1617 Dihedral : 4.509 46.914 1243 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.96 % Allowed : 20.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.25), residues: 1113 helix: 1.59 (0.27), residues: 375 sheet: 1.09 (0.37), residues: 205 loop : -0.34 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 159 HIS 0.004 0.001 HIS C 116 PHE 0.024 0.001 PHE A 361 TYR 0.014 0.001 TYR B 239 ARG 0.006 0.001 ARG B 453 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 406) hydrogen bonds : angle 4.94950 ( 1140) covalent geometry : bond 0.00333 ( 9114) covalent geometry : angle 0.58751 (12339) Misc. bond : bond 0.00094 ( 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 275 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 247 time to evaluate : 1.233 Fit side-chains REVERT: A 4 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7621 (mp0) REVERT: A 12 GLU cc_start: 0.7696 (tt0) cc_final: 0.7432 (tt0) REVERT: A 33 THR cc_start: 0.8020 (t) cc_final: 0.7747 (m) REVERT: A 42 GLU cc_start: 0.7872 (pp20) cc_final: 0.7355 (pp20) REVERT: A 51 ASP cc_start: 0.8239 (t70) cc_final: 0.7846 (t0) REVERT: A 55 ILE cc_start: 0.8727 (mm) cc_final: 0.8409 (mt) REVERT: A 155 ILE cc_start: 0.8391 (mt) cc_final: 0.8149 (tp) REVERT: A 276 SER cc_start: 0.8551 (m) cc_final: 0.8143 (t) REVERT: A 338 ARG cc_start: 0.8065 (mtt180) cc_final: 0.7821 (mtt90) REVERT: A 441 ASP cc_start: 0.8124 (m-30) cc_final: 0.7808 (m-30) REVERT: B 16 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8433 (mmmm) REVERT: B 42 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7979 (mt-10) REVERT: B 177 LYS cc_start: 0.8352 (mtpt) cc_final: 0.8064 (mtmm) REVERT: B 338 ARG cc_start: 0.8082 (mtt180) cc_final: 0.7850 (mtp-110) REVERT: B 345 ARG cc_start: 0.8224 (mmm160) cc_final: 0.7928 (mmm-85) REVERT: B 398 TYR cc_start: 0.8670 (m-80) cc_final: 0.7474 (m-80) REVERT: B 425 ASP cc_start: 0.8123 (t0) cc_final: 0.7761 (t0) REVERT: C 38 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8588 (p) REVERT: C 90 ASN cc_start: 0.8274 (m110) cc_final: 0.8063 (m110) outliers start: 28 outliers final: 15 residues processed: 254 average time/residue: 1.3297 time to fit residues: 357.7738 Evaluate side-chains 260 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 243 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP 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 54 SER Chi-restraints excluded: chain B residue 97 THR 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 72 optimal weight: 0.8980 chunk 73 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 77 optimal weight: 0.0970 chunk 23 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 116 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.141639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.130147 restraints weight = 14205.150| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.00 r_work: 0.3584 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9116 Z= 0.128 Angle : 0.588 8.957 12339 Z= 0.295 Chirality : 0.044 0.185 1356 Planarity : 0.005 0.064 1617 Dihedral : 4.452 46.984 1243 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.54 % Allowed : 20.19 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.25), residues: 1113 helix: 1.66 (0.27), residues: 374 sheet: 1.07 (0.37), residues: 209 loop : -0.30 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 159 HIS 0.005 0.001 HIS C 116 PHE 0.022 0.001 PHE A 361 TYR 0.014 0.001 TYR B 239 ARG 0.008 0.001 ARG D 108 Details of bonding type rmsd hydrogen bonds : bond 0.03623 ( 406) hydrogen bonds : angle 4.91476 ( 1140) covalent geometry : bond 0.00294 ( 9114) covalent geometry : angle 0.58825 (12339) Misc. bond : bond 0.00068 ( 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: 24 poor density : 248 time to evaluate : 0.985 Fit side-chains REVERT: A 4 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7615 (mp0) REVERT: A 33 THR cc_start: 0.8009 (t) cc_final: 0.7725 (m) REVERT: A 42 GLU cc_start: 0.7897 (pp20) cc_final: 0.7365 (pp20) REVERT: A 51 ASP cc_start: 0.8223 (t70) cc_final: 0.7821 (t0) REVERT: A 55 ILE cc_start: 0.8717 (mm) cc_final: 0.8400 (mt) REVERT: A 276 SER cc_start: 0.8532 (m) cc_final: 0.8115 (t) REVERT: A 321 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8150 (mttt) REVERT: A 338 ARG cc_start: 0.8110 (mtt180) cc_final: 0.7883 (mtt90) REVERT: A 441 ASP cc_start: 0.8085 (m-30) cc_final: 0.7791 (m-30) REVERT: B 16 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8431 (mmmm) REVERT: B 42 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7999 (mt-10) REVERT: B 177 LYS cc_start: 0.8351 (mtpt) cc_final: 0.8054 (mtmm) REVERT: B 338 ARG cc_start: 0.8098 (mtt180) cc_final: 0.7857 (mtp-110) REVERT: B 345 ARG cc_start: 0.8238 (mmm160) cc_final: 0.7936 (mmm-85) REVERT: B 398 TYR cc_start: 0.8684 (m-80) cc_final: 0.7544 (m-80) REVERT: B 425 ASP cc_start: 0.8136 (t0) cc_final: 0.7831 (t0) REVERT: B 438 GLU cc_start: 0.7968 (mp0) cc_final: 0.7641 (mp0) REVERT: C 90 ASN cc_start: 0.8248 (m110) cc_final: 0.8032 (m110) REVERT: D 48 ILE cc_start: 0.8603 (mm) cc_final: 0.8401 (mp) outliers start: 24 outliers final: 14 residues processed: 255 average time/residue: 1.4307 time to fit residues: 387.4798 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 : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 321 LYS 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 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 62 LEU Chi-restraints excluded: chain D residue 10 ILE 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 110 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 31 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** 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 = 0.3849 r_free = 0.3849 target = 0.140166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.128756 restraints weight = 14399.352| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.98 r_work: 0.3580 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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 0.038 9116 Z= 0.147 Angle : 0.614 9.043 12339 Z= 0.309 Chirality : 0.045 0.189 1356 Planarity : 0.005 0.068 1617 Dihedral : 4.537 47.525 1243 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.80 % Allowed : 22.41 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.25), residues: 1113 helix: 1.67 (0.27), residues: 374 sheet: 1.08 (0.37), residues: 209 loop : -0.31 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 159 HIS 0.005 0.001 HIS C 116 PHE 0.023 0.001 PHE A 361 TYR 0.014 0.001 TYR B 239 ARG 0.009 0.001 ARG D 108 Details of bonding type rmsd hydrogen bonds : bond 0.03755 ( 406) hydrogen bonds : angle 4.96278 ( 1140) covalent geometry : bond 0.00338 ( 9114) covalent geometry : angle 0.61418 (12339) Misc. bond : bond 0.00087 ( 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 263 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 246 time to evaluate : 0.825 Fit side-chains revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7614 (mp0) REVERT: A 33 THR cc_start: 0.8014 (t) cc_final: 0.7733 (m) REVERT: A 42 GLU cc_start: 0.7912 (pp20) cc_final: 0.7373 (pp20) REVERT: A 51 ASP cc_start: 0.8216 (t70) cc_final: 0.7821 (t0) REVERT: A 55 ILE cc_start: 0.8737 (mm) cc_final: 0.8418 (mt) REVERT: A 276 SER cc_start: 0.8519 (m) cc_final: 0.8107 (t) REVERT: A 321 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8118 (mttt) REVERT: A 338 ARG cc_start: 0.8057 (mtt180) cc_final: 0.7845 (mtt90) REVERT: A 441 ASP cc_start: 0.8084 (m-30) cc_final: 0.7795 (m-30) REVERT: B 16 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8441 (mmmm) REVERT: B 26 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8531 (mttm) REVERT: B 42 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7960 (mt-10) REVERT: B 177 LYS cc_start: 0.8315 (mtpt) cc_final: 0.8035 (mtmm) REVERT: B 338 ARG cc_start: 0.8169 (mtt180) cc_final: 0.7930 (mtp-110) REVERT: B 345 ARG cc_start: 0.8240 (mmm160) cc_final: 0.7927 (mmm-85) REVERT: B 398 TYR cc_start: 0.8673 (m-80) cc_final: 0.7518 (m-80) REVERT: B 425 ASP cc_start: 0.8138 (t0) cc_final: 0.7882 (t0) REVERT: C 90 ASN cc_start: 0.8244 (m110) cc_final: 0.8030 (m110) outliers start: 17 outliers final: 12 residues processed: 253 average time/residue: 1.3710 time to fit residues: 366.0734 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 : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 97 THR 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 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 62 LEU 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 104 optimal weight: 0.4980 chunk 14 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 84 optimal weight: 0.1980 chunk 62 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 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** C 116 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.140743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.129235 restraints weight = 14389.670| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.00 r_work: 0.3580 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2683 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 : 0.607 9.822 12339 Z= 0.305 Chirality : 0.045 0.185 1356 Planarity : 0.005 0.068 1617 Dihedral : 4.545 48.572 1243 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.25), residues: 1113 helix: 1.71 (0.27), residues: 374 sheet: 1.08 (0.37), residues: 209 loop : -0.29 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 159 HIS 0.005 0.001 HIS C 116 PHE 0.022 0.001 PHE A 361 TYR 0.014 0.001 TYR B 239 ARG 0.011 0.001 ARG D 108 Details of bonding type rmsd hydrogen bonds : bond 0.03688 ( 406) hydrogen bonds : angle 4.90363 ( 1140) covalent geometry : bond 0.00311 ( 9114) covalent geometry : angle 0.60669 (12339) Misc. bond : bond 0.00075 ( 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 262 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 242 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: A 33 THR cc_start: 0.8017 (t) cc_final: 0.7737 (m) REVERT: A 42 GLU cc_start: 0.7889 (pp20) cc_final: 0.7346 (pp20) REVERT: A 51 ASP cc_start: 0.8203 (t70) cc_final: 0.7800 (t0) REVERT: A 55 ILE cc_start: 0.8739 (mm) cc_final: 0.8421 (mt) REVERT: A 276 SER cc_start: 0.8481 (m) cc_final: 0.8083 (t) REVERT: A 321 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8128 (mttt) REVERT: A 338 ARG cc_start: 0.8068 (mtt180) cc_final: 0.7861 (mtt90) REVERT: A 441 ASP cc_start: 0.8086 (m-30) cc_final: 0.7826 (m-30) REVERT: B 16 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8445 (mmmm) REVERT: B 42 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7973 (mt-10) REVERT: B 177 LYS cc_start: 0.8336 (mtpt) cc_final: 0.8051 (mtmm) REVERT: B 277 LYS cc_start: 0.8627 (tttt) cc_final: 0.8409 (tttp) REVERT: B 338 ARG cc_start: 0.8119 (mtt180) cc_final: 0.7902 (mtp-110) REVERT: B 339 ASN cc_start: 0.7882 (t0) cc_final: 0.7633 (m110) REVERT: B 345 ARG cc_start: 0.8216 (mmm160) cc_final: 0.7906 (mmm-85) REVERT: B 398 TYR cc_start: 0.8676 (m-80) cc_final: 0.7507 (m-80) REVERT: B 425 ASP cc_start: 0.8126 (t0) cc_final: 0.7839 (t0) REVERT: C 90 ASN cc_start: 0.8247 (m110) cc_final: 0.7891 (m-40) outliers start: 20 outliers final: 12 residues processed: 250 average time/residue: 1.3945 time to fit residues: 367.8060 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 : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 97 THR 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 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 71 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 75 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 C 35 GLN C 116 HIS ** 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 = 0.3858 r_free = 0.3858 target = 0.140734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.129210 restraints weight = 14305.781| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.99 r_work: 0.3584 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2762 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= 0.137 Angle : 0.618 10.185 12339 Z= 0.312 Chirality : 0.045 0.185 1356 Planarity : 0.005 0.068 1617 Dihedral : 4.529 49.739 1243 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.80 % Allowed : 22.09 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.25), residues: 1113 helix: 1.73 (0.27), residues: 375 sheet: 1.04 (0.37), residues: 209 loop : -0.26 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 159 HIS 0.005 0.001 HIS C 116 PHE 0.022 0.001 PHE A 361 TYR 0.015 0.001 TYR B 239 ARG 0.011 0.001 ARG D 108 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 406) hydrogen bonds : angle 4.89409 ( 1140) covalent geometry : bond 0.00318 ( 9114) covalent geometry : angle 0.61828 (12339) Misc. bond : bond 0.00066 ( 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 261 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 244 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7550 (mp0) REVERT: A 33 THR cc_start: 0.8026 (t) cc_final: 0.7750 (m) REVERT: A 42 GLU cc_start: 0.7892 (pp20) cc_final: 0.7343 (pp20) REVERT: A 51 ASP cc_start: 0.8198 (t70) cc_final: 0.7801 (t0) REVERT: A 55 ILE cc_start: 0.8727 (mm) cc_final: 0.8411 (mt) REVERT: A 153 ASP cc_start: 0.8111 (t0) cc_final: 0.7901 (t0) REVERT: A 276 SER cc_start: 0.8470 (m) cc_final: 0.8085 (t) REVERT: B 16 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8444 (mmmm) REVERT: B 42 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7983 (mt-10) REVERT: B 177 LYS cc_start: 0.8344 (mtpt) cc_final: 0.8059 (mtmm) REVERT: B 277 LYS cc_start: 0.8634 (tttt) cc_final: 0.8412 (tttp) REVERT: B 330 PRO cc_start: 0.8776 (Cg_endo) cc_final: 0.8400 (Cg_exo) REVERT: B 338 ARG cc_start: 0.8107 (mtt180) cc_final: 0.7883 (mtp-110) REVERT: B 339 ASN cc_start: 0.7870 (t0) cc_final: 0.7627 (m110) REVERT: B 345 ARG cc_start: 0.8211 (mmm160) cc_final: 0.7907 (mmm-85) REVERT: B 398 TYR cc_start: 0.8682 (m-80) cc_final: 0.7485 (m-80) REVERT: B 425 ASP cc_start: 0.8081 (t0) cc_final: 0.7808 (t0) REVERT: C 90 ASN cc_start: 0.8273 (m110) cc_final: 0.7911 (m-40) outliers start: 17 outliers final: 13 residues processed: 249 average time/residue: 1.3625 time to fit residues: 358.8700 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 : 1.037 ------------------------------------------------------------------------------- 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 16 LYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 130 GLU 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 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 62 optimal weight: 0.0170 chunk 65 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 77 optimal weight: 0.0670 chunk 111 optimal weight: 0.3980 overall best weight: 0.3756 ------------------------------------------------------------------------------- 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 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 = 0.3873 r_free = 0.3873 target = 0.142285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.130807 restraints weight = 14373.330| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.01 r_work: 0.3599 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2804 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= 0.118 Angle : 0.614 11.357 12339 Z= 0.308 Chirality : 0.044 0.173 1356 Planarity : 0.005 0.065 1617 Dihedral : 4.483 48.800 1243 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.69 % Allowed : 22.94 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.25), residues: 1113 helix: 1.80 (0.27), residues: 375 sheet: 1.01 (0.37), residues: 209 loop : -0.22 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 159 HIS 0.005 0.001 HIS C 116 PHE 0.020 0.001 PHE A 361 TYR 0.014 0.001 TYR B 239 ARG 0.011 0.001 ARG D 108 Details of bonding type rmsd hydrogen bonds : bond 0.03481 ( 406) hydrogen bonds : angle 4.82225 ( 1140) covalent geometry : bond 0.00272 ( 9114) covalent geometry : angle 0.61354 (12339) Misc. bond : bond 0.00045 ( 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 260 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 244 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7541 (mp0) REVERT: A 33 THR cc_start: 0.8007 (t) cc_final: 0.7730 (m) REVERT: A 42 GLU cc_start: 0.7909 (pp20) cc_final: 0.7347 (pp20) REVERT: A 51 ASP cc_start: 0.8185 (t70) cc_final: 0.7792 (t0) REVERT: A 55 ILE cc_start: 0.8716 (mm) cc_final: 0.8395 (mt) REVERT: A 276 SER cc_start: 0.8460 (m) cc_final: 0.8107 (t) REVERT: B 16 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8447 (mmmm) REVERT: B 177 LYS cc_start: 0.8311 (mtpt) cc_final: 0.8018 (mtmm) REVERT: B 224 THR cc_start: 0.8536 (m) cc_final: 0.8097 (p) REVERT: B 277 LYS cc_start: 0.8648 (tttt) cc_final: 0.8423 (tttp) REVERT: B 330 PRO cc_start: 0.8762 (Cg_endo) cc_final: 0.8387 (Cg_exo) REVERT: B 338 ARG cc_start: 0.8070 (mtt180) cc_final: 0.7838 (mtp-110) REVERT: B 345 ARG cc_start: 0.8215 (mmm160) cc_final: 0.7908 (mmm-85) REVERT: B 398 TYR cc_start: 0.8665 (m-80) cc_final: 0.7543 (m-80) REVERT: B 425 ASP cc_start: 0.8092 (t0) cc_final: 0.7837 (t0) REVERT: C 90 ASN cc_start: 0.8268 (m110) cc_final: 0.7907 (m-40) outliers start: 16 outliers final: 10 residues processed: 250 average time/residue: 1.4692 time to fit residues: 388.6426 Evaluate side-chains 248 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 237 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 16 LYS 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 50 THR Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 50 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 2 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 16 optimal weight: 0.0050 chunk 23 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- 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 = 0.3862 r_free = 0.3862 target = 0.141105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.129617 restraints weight = 14462.706| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.00 r_work: 0.3589 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9116 Z= 0.136 Angle : 0.630 11.447 12339 Z= 0.315 Chirality : 0.045 0.181 1356 Planarity : 0.005 0.064 1617 Dihedral : 4.501 48.871 1243 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.48 % Allowed : 23.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.25), residues: 1113 helix: 1.82 (0.27), residues: 375 sheet: 1.02 (0.36), residues: 211 loop : -0.18 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 159 HIS 0.005 0.001 HIS C 116 PHE 0.022 0.001 PHE A 361 TYR 0.014 0.001 TYR B 239 ARG 0.011 0.001 ARG D 108 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 406) hydrogen bonds : angle 4.84524 ( 1140) covalent geometry : bond 0.00316 ( 9114) covalent geometry : angle 0.63042 (12339) Misc. bond : bond 0.00062 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10274.26 seconds wall clock time: 178 minutes 16.63 seconds (10696.63 seconds total)