Starting phenix.real_space_refine on Sat Dec 28 18:05:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v1y_42892/12_2024/8v1y_42892.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v1y_42892/12_2024/8v1y_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_42892/12_2024/8v1y_42892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v1y_42892/12_2024/8v1y_42892.map" model { file = "/net/cci-nas-00/data/ceres_data/8v1y_42892/12_2024/8v1y_42892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v1y_42892/12_2024/8v1y_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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 Classifications: {'RNA': 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 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 6.57, per 1000 atoms: 0.74 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: 2.45 Conformation dependent library (CDL) restraints added in 1.0 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: 1.18 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: 3.02 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2996 1.34 - 1.46: 1585 1.46 - 1.57: 4439 1.57 - 1.69: 2 1.69 - 1.81: 92 Bond restraints: 9114 Sorted by residual: bond pdb=" C4 AMP A 501 " pdb=" C5 AMP A 501 " ideal model delta sigma weight residual 1.490 1.376 0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" C4 AMP B 501 " pdb=" C5 AMP B 501 " ideal model delta sigma weight residual 1.490 1.376 0.114 2.00e-02 2.50e+03 3.24e+01 bond pdb=" C5 AMP A 501 " pdb=" C6 AMP A 501 " ideal model delta sigma weight residual 1.490 1.404 0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C5 AMP B 501 " pdb=" C6 AMP B 501 " ideal model delta sigma weight residual 1.490 1.404 0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C8 AMP B 501 " pdb=" N7 AMP B 501 " ideal model delta sigma weight residual 1.350 1.307 0.043 2.00e-02 2.50e+03 4.68e+00 ... (remaining 9109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 12187 1.87 - 3.74: 125 3.74 - 5.61: 19 5.61 - 7.48: 4 7.48 - 9.34: 4 Bond angle restraints: 12339 Sorted by residual: angle pdb=" N VAL D 97 " pdb=" CA VAL D 97 " pdb=" C VAL D 97 " ideal model delta sigma weight residual 112.96 109.12 3.84 1.00e+00 1.00e+00 1.47e+01 angle pdb=" N1 AMP B 501 " pdb=" C2 AMP B 501 " pdb=" N3 AMP B 501 " ideal model delta sigma weight residual 120.00 129.34 -9.34 3.00e+00 1.11e-01 9.70e+00 angle pdb=" N1 AMP A 501 " pdb=" C2 AMP A 501 " pdb=" N3 AMP A 501 " ideal model delta sigma weight residual 120.00 129.25 -9.25 3.00e+00 1.11e-01 9.50e+00 angle pdb=" C2 AMP A 501 " pdb=" N3 AMP A 501 " pdb=" C4 AMP A 501 " ideal model delta sigma weight residual 120.00 110.80 9.20 3.00e+00 1.11e-01 9.40e+00 angle pdb=" C2 AMP B 501 " pdb=" N3 AMP B 501 " pdb=" C4 AMP B 501 " ideal model delta sigma weight residual 120.00 110.81 9.19 3.00e+00 1.11e-01 9.38e+00 ... (remaining 12334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 5011 17.40 - 34.81: 391 34.81 - 52.21: 53 52.21 - 69.61: 18 69.61 - 87.02: 6 Dihedral angle restraints: 5479 sinusoidal: 2206 harmonic: 3273 Sorted by residual: dihedral pdb=" C1' AMP A 501 " pdb=" C4' AMP A 501 " pdb=" O4' AMP A 501 " pdb=" C5' AMP A 501 " ideal model delta sinusoidal sigma weight residual -123.00 -159.56 36.56 1 8.00e+00 1.56e-02 2.95e+01 dihedral pdb=" CA THR B 228 " pdb=" C THR B 228 " pdb=" N MET B 229 " pdb=" CA MET B 229 " ideal model delta harmonic sigma weight residual -180.00 -162.71 -17.29 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA TYR A 320 " pdb=" C TYR A 320 " pdb=" N LYS A 321 " pdb=" CA LYS A 321 " ideal model delta harmonic sigma weight residual 180.00 163.13 16.87 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 5476 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 853 0.031 - 0.062: 326 0.062 - 0.093: 97 0.093 - 0.123: 69 0.123 - 0.154: 11 Chirality restraints: 1356 Sorted by residual: chirality pdb=" C2' AMP B 501 " pdb=" C1' AMP B 501 " pdb=" C3' AMP B 501 " pdb=" O2' AMP B 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.60 -0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA PHE B 361 " pdb=" N PHE B 361 " pdb=" C PHE B 361 " pdb=" CB PHE B 361 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.82e-01 chirality pdb=" CA VAL A 324 " pdb=" N VAL A 324 " pdb=" C VAL A 324 " pdb=" CB VAL A 324 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.60e-01 ... (remaining 1353 not shown) Planarity restraints: 1617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 314 " -0.034 5.00e-02 4.00e+02 5.20e-02 4.32e+00 pdb=" N PRO B 315 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 315 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 315 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 128 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.87e+00 pdb=" N PRO B 129 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 129 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 129 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 184 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A 185 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 185 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 185 " 0.023 5.00e-02 4.00e+02 ... (remaining 1614 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2071 2.79 - 3.32: 8365 3.32 - 3.85: 14654 3.85 - 4.37: 17539 4.37 - 4.90: 29674 Nonbonded interactions: 72303 Sorted by model distance: nonbonded pdb=" OG SER B 319 " pdb=" OD2 ASP B 363 " model vdw 2.268 3.040 nonbonded pdb=" NH2 ARG D 84 " pdb=" O GLY D 111 " model vdw 2.277 3.120 nonbonded pdb=" OG1 THR B 316 " pdb=" OG SER B 319 " model vdw 2.282 3.040 nonbonded pdb=" O ASN C 88 " pdb=" NE2 GLN C 95 " model vdw 2.294 3.120 nonbonded pdb=" OE2 GLU B 416 " pdb=" NH1 ARG B 448 " model vdw 2.301 3.120 ... (remaining 72298 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 398 or resid 406 through 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: 1.590 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 25.340 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 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:13.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.270 ------------------------------------------------------------------------------- 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 9114 Z= 0.215 Angle : 0.515 9.344 12339 Z= 0.259 Chirality : 0.042 0.154 1356 Planarity : 0.004 0.052 1617 Dihedral : 12.809 87.017 3371 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 *********************** 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 : 1.026 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: 1.4497 time to fit residues: 480.6887 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 : 1.082 ------------------------------------------------------------------------------- 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** D 35 GLN ** D 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9114 Z= 0.330 Angle : 0.594 7.562 12339 Z= 0.311 Chirality : 0.047 0.191 1356 Planarity : 0.006 0.055 1617 Dihedral : 4.970 47.099 1243 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.48 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: 0.84 (0.25), residues: 1113 helix: 1.35 (0.27), residues: 377 sheet: 1.19 (0.36), residues: 204 loop : -0.21 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 159 HIS 0.005 0.001 HIS D 92 PHE 0.021 0.002 PHE A 361 TYR 0.016 0.002 TYR B 239 ARG 0.008 0.001 ARG C 108 *********************** 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: 15 poor density : 259 time to evaluate : 1.176 Fit side-chains REVERT: A 2 SER cc_start: 0.8168 (t) cc_final: 0.7935 (p) REVERT: A 4 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8247 (mp0) REVERT: A 12 GLU cc_start: 0.8552 (tt0) cc_final: 0.8279 (tt0) REVERT: A 42 GLU cc_start: 0.8808 (pp20) cc_final: 0.8386 (pp20) REVERT: A 154 ASP cc_start: 0.8533 (p0) cc_final: 0.8275 (p0) REVERT: A 155 ILE cc_start: 0.8647 (mt) cc_final: 0.8445 (tp) REVERT: A 269 MET cc_start: 0.8811 (ttp) cc_final: 0.8516 (ttp) REVERT: A 276 SER cc_start: 0.8924 (m) cc_final: 0.8593 (t) REVERT: A 338 ARG cc_start: 0.9042 (mtt180) cc_final: 0.8766 (mtt180) REVERT: A 357 ILE cc_start: 0.8741 (mp) cc_final: 0.8478 (pt) REVERT: B 32 VAL cc_start: 0.8812 (t) cc_final: 0.8569 (p) REVERT: B 42 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8647 (mt-10) REVERT: B 176 VAL cc_start: 0.8549 (m) cc_final: 0.8338 (t) REVERT: B 177 LYS cc_start: 0.8680 (mtpt) cc_final: 0.8176 (mtmm) REVERT: B 277 LYS cc_start: 0.8629 (tttt) cc_final: 0.8401 (tttp) REVERT: B 345 ARG cc_start: 0.8992 (mmm160) cc_final: 0.8588 (mmm-85) REVERT: B 353 LYS cc_start: 0.9042 (mttt) cc_final: 0.8834 (mttt) REVERT: B 398 TYR cc_start: 0.9004 (m-80) cc_final: 0.7906 (m-80) REVERT: B 416 GLU cc_start: 0.8959 (tp30) cc_final: 0.8722 (tt0) REVERT: B 425 ASP cc_start: 0.8764 (t0) cc_final: 0.8260 (t0) REVERT: B 450 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8136 (mt-10) REVERT: C 90 ASN cc_start: 0.8685 (m110) cc_final: 0.8477 (m110) REVERT: D 76 GLU cc_start: 0.9162 (tp30) cc_final: 0.8944 (tp30) outliers start: 15 outliers final: 10 residues processed: 261 average time/residue: 1.3400 time to fit residues: 370.5622 Evaluate side-chains 259 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 249 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 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 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 84 optimal weight: 0.0170 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 0.0980 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 overall best weight: 0.4218 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9114 Z= 0.175 Angle : 0.554 8.216 12339 Z= 0.283 Chirality : 0.044 0.192 1356 Planarity : 0.005 0.059 1617 Dihedral : 4.966 54.880 1243 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.11 % Allowed : 18.39 % Favored : 79.49 % 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: 0.90 (0.25), residues: 1113 helix: 1.52 (0.27), residues: 375 sheet: 1.17 (0.37), residues: 206 loop : -0.27 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 159 HIS 0.006 0.001 HIS C 116 PHE 0.029 0.001 PHE A 361 TYR 0.013 0.001 TYR B 239 ARG 0.005 0.000 ARG C 108 *********************** 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 274 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 254 time to evaluate : 1.119 Fit side-chains REVERT: A 1 MET cc_start: 0.8263 (mtm) cc_final: 0.8026 (ttm) REVERT: A 2 SER cc_start: 0.8142 (t) cc_final: 0.7856 (p) REVERT: A 4 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8237 (mp0) REVERT: A 12 GLU cc_start: 0.8525 (tt0) cc_final: 0.8255 (tt0) REVERT: A 42 GLU cc_start: 0.8772 (pp20) cc_final: 0.8372 (pp20) REVERT: A 55 ILE cc_start: 0.8649 (mm) cc_final: 0.8409 (mt) REVERT: A 154 ASP cc_start: 0.8502 (p0) cc_final: 0.8231 (p0) REVERT: A 155 ILE cc_start: 0.8733 (mt) cc_final: 0.8478 (tp) REVERT: A 269 MET cc_start: 0.8808 (ttp) cc_final: 0.8527 (ttp) REVERT: A 276 SER cc_start: 0.8895 (m) cc_final: 0.8561 (t) REVERT: A 338 ARG cc_start: 0.9071 (mtt180) cc_final: 0.8794 (mtt180) REVERT: A 357 ILE cc_start: 0.8745 (mp) cc_final: 0.8526 (pt) REVERT: A 441 ASP cc_start: 0.8908 (m-30) cc_final: 0.8594 (m-30) REVERT: B 42 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8648 (mt-10) REVERT: B 177 LYS cc_start: 0.8651 (mtpt) cc_final: 0.8199 (mtmm) REVERT: B 277 LYS cc_start: 0.8608 (tttt) cc_final: 0.8390 (tttp) REVERT: B 345 ARG cc_start: 0.8982 (mmm160) cc_final: 0.8591 (mmm-85) REVERT: B 353 LYS cc_start: 0.9047 (mttt) cc_final: 0.8838 (mttt) REVERT: B 398 TYR cc_start: 0.8938 (m-80) cc_final: 0.7883 (m-80) REVERT: B 416 GLU cc_start: 0.8934 (tp30) cc_final: 0.8690 (tt0) REVERT: B 425 ASP cc_start: 0.8784 (t0) cc_final: 0.8330 (t0) REVERT: B 438 GLU cc_start: 0.8906 (mp0) cc_final: 0.8646 (mp0) REVERT: B 450 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8116 (mt-10) REVERT: C 90 ASN cc_start: 0.8654 (m110) cc_final: 0.8452 (m110) outliers start: 20 outliers final: 10 residues processed: 259 average time/residue: 1.3497 time to fit residues: 370.2224 Evaluate side-chains 254 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 244 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 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 100 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9114 Z= 0.252 Angle : 0.571 8.365 12339 Z= 0.295 Chirality : 0.045 0.198 1356 Planarity : 0.005 0.060 1617 Dihedral : 5.031 54.078 1243 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.33 % Allowed : 18.82 % Favored : 78.86 % 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: 1.51 (0.27), residues: 376 sheet: 1.15 (0.37), residues: 205 loop : -0.31 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 159 HIS 0.004 0.001 HIS C 103 PHE 0.026 0.001 PHE A 361 TYR 0.015 0.001 TYR B 239 ARG 0.008 0.001 ARG C 108 *********************** 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 276 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 254 time to evaluate : 1.120 Fit side-chains REVERT: A 1 MET cc_start: 0.8254 (mtm) cc_final: 0.8006 (ttm) REVERT: A 2 SER cc_start: 0.8162 (t) cc_final: 0.7880 (p) REVERT: A 4 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8220 (mp0) REVERT: A 12 GLU cc_start: 0.8543 (tt0) cc_final: 0.8275 (tt0) REVERT: A 42 GLU cc_start: 0.8784 (pp20) cc_final: 0.8368 (pp20) REVERT: A 55 ILE cc_start: 0.8661 (mm) cc_final: 0.8427 (mt) REVERT: A 154 ASP cc_start: 0.8545 (p0) cc_final: 0.8220 (p0) REVERT: A 155 ILE cc_start: 0.8734 (mt) cc_final: 0.8478 (tp) REVERT: A 269 MET cc_start: 0.8813 (ttp) cc_final: 0.8519 (ttp) REVERT: A 276 SER cc_start: 0.8920 (m) cc_final: 0.8581 (t) REVERT: A 338 ARG cc_start: 0.9076 (mtt180) cc_final: 0.8808 (mtt180) REVERT: A 357 ILE cc_start: 0.8750 (mp) cc_final: 0.8514 (pt) REVERT: B 42 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8651 (mt-10) REVERT: B 177 LYS cc_start: 0.8664 (mtpt) cc_final: 0.8215 (mtmm) REVERT: B 277 LYS cc_start: 0.8617 (tttt) cc_final: 0.8400 (tttp) REVERT: B 345 ARG cc_start: 0.9010 (mmm160) cc_final: 0.8632 (mmm-85) REVERT: B 398 TYR cc_start: 0.9002 (m-80) cc_final: 0.7947 (m-80) REVERT: B 416 GLU cc_start: 0.8961 (tp30) cc_final: 0.8716 (tt0) REVERT: B 425 ASP cc_start: 0.8800 (t0) cc_final: 0.8354 (t0) REVERT: B 438 GLU cc_start: 0.8935 (mp0) cc_final: 0.8700 (mp0) REVERT: B 450 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8110 (mt-10) REVERT: C 90 ASN cc_start: 0.8681 (m110) cc_final: 0.8475 (m110) REVERT: C 108 ARG cc_start: 0.8776 (ptt-90) cc_final: 0.8515 (ptt-90) outliers start: 22 outliers final: 17 residues processed: 258 average time/residue: 1.4233 time to fit residues: 388.5720 Evaluate side-chains 259 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 242 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 A residue 446 LEU 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 D residue 33 SER Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 100 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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** B 278 ASN 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9114 Z= 0.319 Angle : 0.604 8.941 12339 Z= 0.311 Chirality : 0.046 0.210 1356 Planarity : 0.005 0.062 1617 Dihedral : 5.147 51.965 1243 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.17 % Allowed : 19.45 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.72 (0.25), residues: 1113 helix: 1.40 (0.27), residues: 377 sheet: 1.08 (0.37), residues: 205 loop : -0.40 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 159 HIS 0.006 0.001 HIS C 116 PHE 0.027 0.002 PHE A 361 TYR 0.017 0.002 TYR B 239 ARG 0.008 0.001 ARG B 453 *********************** 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 277 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 247 time to evaluate : 0.985 Fit side-chains REVERT: A 2 SER cc_start: 0.8151 (t) cc_final: 0.7878 (p) REVERT: A 4 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8235 (mp0) REVERT: A 12 GLU cc_start: 0.8562 (tt0) cc_final: 0.8295 (tt0) REVERT: A 42 GLU cc_start: 0.8819 (pp20) cc_final: 0.8406 (pp20) REVERT: A 55 ILE cc_start: 0.8668 (mm) cc_final: 0.8446 (mt) REVERT: A 154 ASP cc_start: 0.8580 (p0) cc_final: 0.8315 (p0) REVERT: A 155 ILE cc_start: 0.8737 (mt) cc_final: 0.8478 (tp) REVERT: A 276 SER cc_start: 0.8932 (m) cc_final: 0.8592 (t) REVERT: A 338 ARG cc_start: 0.9098 (mtt180) cc_final: 0.8828 (mtt180) REVERT: A 357 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8493 (pt) REVERT: A 441 ASP cc_start: 0.8914 (m-30) cc_final: 0.8623 (m-30) REVERT: B 42 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8641 (mt-10) REVERT: B 345 ARG cc_start: 0.9011 (mmm160) cc_final: 0.8642 (mmm-85) REVERT: B 398 TYR cc_start: 0.9013 (m-80) cc_final: 0.7873 (m-80) REVERT: B 416 GLU cc_start: 0.8966 (tp30) cc_final: 0.8719 (tt0) REVERT: B 425 ASP cc_start: 0.8815 (t0) cc_final: 0.8376 (t0) REVERT: B 438 GLU cc_start: 0.8978 (mp0) cc_final: 0.8751 (mp0) REVERT: B 450 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8109 (mt-10) REVERT: C 90 ASN cc_start: 0.8706 (m110) cc_final: 0.8481 (m110) outliers start: 30 outliers final: 16 residues processed: 257 average time/residue: 1.5008 time to fit residues: 410.0764 Evaluate side-chains 264 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 247 time to evaluate : 1.119 ------------------------------------------------------------------------------- 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 357 ILE Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain B residue 49 MET 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 33 SER Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 58 HIS Chi-restraints excluded: chain D residue 66 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 89 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 265 ASN C 116 HIS ** D 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9114 Z= 0.233 Angle : 0.591 8.766 12339 Z= 0.304 Chirality : 0.045 0.197 1356 Planarity : 0.005 0.065 1617 Dihedral : 5.150 53.008 1243 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % 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: 0.78 (0.25), residues: 1113 helix: 1.47 (0.27), residues: 377 sheet: 1.07 (0.37), residues: 205 loop : -0.37 (0.26), residues: 531 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 0.024 0.001 PHE A 361 TYR 0.014 0.001 TYR B 239 ARG 0.009 0.001 ARG C 108 *********************** 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: 24 poor density : 250 time to evaluate : 1.030 Fit side-chains REVERT: A 2 SER cc_start: 0.8107 (t) cc_final: 0.7868 (p) REVERT: A 4 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8242 (mp0) REVERT: A 12 GLU cc_start: 0.8548 (tt0) cc_final: 0.8282 (tt0) REVERT: A 42 GLU cc_start: 0.8793 (pp20) cc_final: 0.8389 (pp20) REVERT: A 55 ILE cc_start: 0.8665 (mm) cc_final: 0.8441 (mt) REVERT: A 154 ASP cc_start: 0.8578 (p0) cc_final: 0.8247 (p0) REVERT: A 155 ILE cc_start: 0.8740 (mt) cc_final: 0.8490 (tp) REVERT: A 276 SER cc_start: 0.8921 (m) cc_final: 0.8578 (t) REVERT: A 338 ARG cc_start: 0.9107 (mtt180) cc_final: 0.8834 (mtt180) REVERT: A 357 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8483 (pt) REVERT: A 441 ASP cc_start: 0.8896 (m-30) cc_final: 0.8612 (m-30) REVERT: B 42 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8646 (mt-10) REVERT: B 345 ARG cc_start: 0.9010 (mmm160) cc_final: 0.8623 (mmm-85) REVERT: B 396 ASN cc_start: 0.9020 (t0) cc_final: 0.8649 (t0) REVERT: B 398 TYR cc_start: 0.8975 (m-80) cc_final: 0.7739 (m-80) REVERT: B 416 GLU cc_start: 0.8941 (tp30) cc_final: 0.8633 (tt0) REVERT: B 425 ASP cc_start: 0.8810 (t0) cc_final: 0.8342 (t0) REVERT: B 438 GLU cc_start: 0.8917 (mp0) cc_final: 0.8716 (mp0) REVERT: B 450 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8108 (mt-10) REVERT: C 90 ASN cc_start: 0.8658 (m110) cc_final: 0.8437 (m110) outliers start: 24 outliers final: 13 residues processed: 258 average time/residue: 1.3993 time to fit residues: 381.6302 Evaluate side-chains 258 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 244 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 73 SER 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 33 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 0.0970 chunk 79 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 265 ASN 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9114 Z= 0.203 Angle : 0.589 9.282 12339 Z= 0.301 Chirality : 0.044 0.187 1356 Planarity : 0.005 0.067 1617 Dihedral : 5.123 52.687 1243 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.11 % Allowed : 20.61 % 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: 0.85 (0.25), residues: 1113 helix: 1.57 (0.27), residues: 376 sheet: 1.09 (0.37), residues: 205 loop : -0.35 (0.26), residues: 532 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 0.009 0.001 ARG D 108 *********************** 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 268 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 248 time to evaluate : 1.098 Fit side-chains REVERT: A 4 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8235 (mp0) REVERT: A 42 GLU cc_start: 0.8780 (pp20) cc_final: 0.8377 (pp20) REVERT: A 55 ILE cc_start: 0.8672 (mm) cc_final: 0.8450 (mt) REVERT: A 154 ASP cc_start: 0.8517 (p0) cc_final: 0.8220 (p0) REVERT: A 155 ILE cc_start: 0.8715 (mt) cc_final: 0.8470 (tp) REVERT: A 276 SER cc_start: 0.8923 (m) cc_final: 0.8565 (t) REVERT: A 338 ARG cc_start: 0.9112 (mtt180) cc_final: 0.8838 (mtt180) REVERT: A 357 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8471 (pt) REVERT: A 441 ASP cc_start: 0.8881 (m-30) cc_final: 0.8608 (m-30) REVERT: B 42 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8649 (mt-10) REVERT: B 103 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8449 (mtt180) REVERT: B 123 ASP cc_start: 0.9007 (m-30) cc_final: 0.8685 (p0) REVERT: B 330 PRO cc_start: 0.8961 (Cg_endo) cc_final: 0.8644 (Cg_exo) REVERT: B 345 ARG cc_start: 0.9011 (mmm160) cc_final: 0.8628 (mmm-85) REVERT: B 396 ASN cc_start: 0.9014 (t0) cc_final: 0.8659 (t0) REVERT: B 398 TYR cc_start: 0.8940 (m-80) cc_final: 0.7613 (m-80) REVERT: B 416 GLU cc_start: 0.8935 (tp30) cc_final: 0.8636 (tt0) REVERT: B 425 ASP cc_start: 0.8806 (t0) cc_final: 0.8410 (t0) REVERT: B 450 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8119 (mt-10) REVERT: C 90 ASN cc_start: 0.8646 (m110) cc_final: 0.8430 (m110) outliers start: 20 outliers final: 13 residues processed: 253 average time/residue: 1.4553 time to fit residues: 388.4693 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 : 0.996 ------------------------------------------------------------------------------- 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 357 ILE Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 103 ARG 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 33 SER 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 64 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9114 Z= 0.252 Angle : 0.624 9.227 12339 Z= 0.319 Chirality : 0.045 0.194 1356 Planarity : 0.005 0.067 1617 Dihedral : 5.178 50.850 1243 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.11 % Allowed : 21.04 % Favored : 76.85 % 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: 1.55 (0.27), residues: 376 sheet: 1.06 (0.37), residues: 207 loop : -0.35 (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 0.023 0.001 PHE A 361 TYR 0.014 0.001 TYR B 239 ARG 0.010 0.001 ARG D 108 *********************** 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 265 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 245 time to evaluate : 1.303 Fit side-chains REVERT: A 4 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8237 (mp0) REVERT: A 42 GLU cc_start: 0.8798 (pp20) cc_final: 0.8388 (pp20) REVERT: A 55 ILE cc_start: 0.8672 (mm) cc_final: 0.8452 (mt) REVERT: A 154 ASP cc_start: 0.8562 (p0) cc_final: 0.8237 (p0) REVERT: A 155 ILE cc_start: 0.8739 (mt) cc_final: 0.8491 (tp) REVERT: A 276 SER cc_start: 0.8925 (m) cc_final: 0.8565 (t) REVERT: A 338 ARG cc_start: 0.9110 (mtt180) cc_final: 0.8840 (mtt180) REVERT: A 357 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8446 (pt) REVERT: A 441 ASP cc_start: 0.8885 (m-30) cc_final: 0.8633 (m-30) REVERT: B 42 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8650 (mt-10) REVERT: B 103 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8440 (mtt180) REVERT: B 330 PRO cc_start: 0.8972 (Cg_endo) cc_final: 0.8657 (Cg_exo) REVERT: B 345 ARG cc_start: 0.9014 (mmm160) cc_final: 0.8628 (mmm-85) REVERT: B 398 TYR cc_start: 0.9015 (m-80) cc_final: 0.7762 (m-80) REVERT: B 416 GLU cc_start: 0.8940 (tp30) cc_final: 0.8605 (tt0) REVERT: B 425 ASP cc_start: 0.8810 (t0) cc_final: 0.8363 (t0) REVERT: B 450 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8107 (mt-10) REVERT: C 90 ASN cc_start: 0.8653 (m110) cc_final: 0.8432 (m110) REVERT: C 108 ARG cc_start: 0.8725 (ptt-90) cc_final: 0.8512 (ptt-90) outliers start: 20 outliers final: 14 residues processed: 250 average time/residue: 1.4203 time to fit residues: 375.0380 Evaluate side-chains 262 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 246 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 357 ILE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 103 ARG 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 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 94 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 106 optimal weight: 0.0170 overall best weight: 0.7218 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9114 Z= 0.223 Angle : 0.628 11.052 12339 Z= 0.317 Chirality : 0.045 0.187 1356 Planarity : 0.005 0.070 1617 Dihedral : 5.247 51.144 1243 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.22 % Allowed : 21.99 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.87 (0.25), residues: 1113 helix: 1.63 (0.27), residues: 375 sheet: 1.03 (0.37), residues: 203 loop : -0.32 (0.26), residues: 535 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 *********************** 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 267 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 246 time to evaluate : 1.032 Fit side-chains REVERT: A 42 GLU cc_start: 0.8789 (pp20) cc_final: 0.8383 (pp20) REVERT: A 55 ILE cc_start: 0.8672 (mm) cc_final: 0.8451 (mt) REVERT: A 154 ASP cc_start: 0.8520 (p0) cc_final: 0.8201 (p0) REVERT: A 155 ILE cc_start: 0.8739 (mt) cc_final: 0.8488 (tp) REVERT: A 276 SER cc_start: 0.8925 (m) cc_final: 0.8561 (t) REVERT: A 338 ARG cc_start: 0.9114 (mtt180) cc_final: 0.8843 (mtt180) REVERT: A 357 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8443 (pt) REVERT: A 441 ASP cc_start: 0.8875 (m-30) cc_final: 0.8625 (m-30) REVERT: B 42 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8655 (mt-10) REVERT: B 103 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.8440 (mtt180) REVERT: B 123 ASP cc_start: 0.9018 (m-30) cc_final: 0.8717 (p0) REVERT: B 330 PRO cc_start: 0.8973 (Cg_endo) cc_final: 0.8654 (Cg_exo) REVERT: B 345 ARG cc_start: 0.9012 (mmm160) cc_final: 0.8626 (mmm-85) REVERT: B 398 TYR cc_start: 0.8996 (m-80) cc_final: 0.7871 (m-80) REVERT: B 416 GLU cc_start: 0.8922 (tp30) cc_final: 0.8599 (tt0) REVERT: B 425 ASP cc_start: 0.8807 (t0) cc_final: 0.8375 (t0) REVERT: B 450 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8119 (mt-10) REVERT: C 90 ASN cc_start: 0.8638 (m110) cc_final: 0.8415 (m110) outliers start: 21 outliers final: 14 residues processed: 251 average time/residue: 1.4521 time to fit residues: 384.1371 Evaluate side-chains 257 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 241 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 357 ILE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 103 ARG 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 33 SER Chi-restraints excluded: chain D residue 50 THR 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 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 111 optimal weight: 0.0270 chunk 102 optimal weight: 0.0980 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 70 optimal weight: 0.4980 chunk 94 optimal weight: 0.2980 overall best weight: 0.3238 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9114 Z= 0.175 Angle : 0.619 11.489 12339 Z= 0.315 Chirality : 0.044 0.169 1356 Planarity : 0.005 0.067 1617 Dihedral : 5.212 51.705 1243 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.90 % Allowed : 21.67 % 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 (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: 0.92 (0.25), residues: 1113 helix: 1.70 (0.27), residues: 376 sheet: 0.95 (0.36), residues: 207 loop : -0.28 (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 0.019 0.001 PHE A 361 TYR 0.013 0.001 TYR B 239 ARG 0.011 0.001 ARG D 108 ********************** 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 265 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 247 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8251 (mp0) REVERT: A 42 GLU cc_start: 0.8756 (pp20) cc_final: 0.8343 (pp20) REVERT: A 51 ASP cc_start: 0.8868 (t70) cc_final: 0.8596 (t0) REVERT: A 55 ILE cc_start: 0.8663 (mm) cc_final: 0.8437 (mt) REVERT: A 154 ASP cc_start: 0.8458 (p0) cc_final: 0.8179 (p0) REVERT: A 155 ILE cc_start: 0.8715 (mt) cc_final: 0.8474 (tp) REVERT: A 276 SER cc_start: 0.8890 (m) cc_final: 0.8554 (t) REVERT: A 338 ARG cc_start: 0.9116 (mtt180) cc_final: 0.8843 (mtt180) REVERT: A 357 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8448 (pt) REVERT: A 441 ASP cc_start: 0.8854 (m-30) cc_final: 0.8620 (m-30) REVERT: B 103 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.8421 (mtt180) REVERT: B 123 ASP cc_start: 0.9008 (m-30) cc_final: 0.8764 (p0) REVERT: B 330 PRO cc_start: 0.8955 (Cg_endo) cc_final: 0.8625 (Cg_exo) REVERT: B 339 ASN cc_start: 0.8396 (t0) cc_final: 0.8046 (m110) REVERT: B 345 ARG cc_start: 0.9009 (mmm160) cc_final: 0.8624 (mmm-85) REVERT: B 398 TYR cc_start: 0.8923 (m-80) cc_final: 0.7781 (m-80) REVERT: B 416 GLU cc_start: 0.8896 (tp30) cc_final: 0.8573 (tt0) REVERT: B 425 ASP cc_start: 0.8798 (t0) cc_final: 0.8409 (t0) REVERT: B 450 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8088 (mt-10) REVERT: C 90 ASN cc_start: 0.8585 (m110) cc_final: 0.8215 (m-40) outliers start: 18 outliers final: 11 residues processed: 252 average time/residue: 1.4313 time to fit residues: 381.6920 Evaluate side-chains 256 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 243 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 103 ARG 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 114 LEU 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 27 optimal weight: 0.0980 chunk 81 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 11 optimal weight: 0.0270 chunk 16 optimal weight: 0.0670 chunk 78 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.141978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.130508 restraints weight = 14120.554| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.99 r_work: 0.3604 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9114 Z= 0.178 Angle : 0.622 11.298 12339 Z= 0.315 Chirality : 0.044 0.170 1356 Planarity : 0.005 0.068 1617 Dihedral : 5.150 50.398 1243 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.59 % Allowed : 23.04 % 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: 0.90 (0.25), residues: 1113 helix: 1.60 (0.27), residues: 382 sheet: 0.92 (0.35), residues: 212 loop : -0.26 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 159 HIS 0.004 0.001 HIS C 116 PHE 0.018 0.001 PHE A 361 TYR 0.013 0.001 TYR B 239 ARG 0.012 0.001 ARG D 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5625.27 seconds wall clock time: 100 minutes 32.63 seconds (6032.63 seconds total)