Starting phenix.real_space_refine on Thu Jun 5 06:24:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qv5_14167/06_2025/7qv5_14167_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qv5_14167/06_2025/7qv5_14167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qv5_14167/06_2025/7qv5_14167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qv5_14167/06_2025/7qv5_14167.map" model { file = "/net/cci-nas-00/data/ceres_data/7qv5_14167/06_2025/7qv5_14167_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qv5_14167/06_2025/7qv5_14167_trim.cif" } resolution = 3.0 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= 0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians C 1638 2.51 5 N 495 2.21 5 O 432 1.98 5 H 2997 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 5562 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 271 Classifications: {'peptide': 17} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 16} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 239 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 106 Classifications: {'peptide': 7} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 6} Restraints were copied for chains: D, G, J, M, P, S, V, Y, E, H, K, N, Q, T, W, Z, F, I, L, O, R, U, X, a Time building chain proxies: 2.26, per 1000 atoms: 0.41 Number of scatterers: 5562 At special positions: 0 Unit cell: (114.75, 123.25, 29.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 432 8.00 N 495 7.00 C 1638 6.00 H 2997 1.00 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=18, symmetry=0 Number of additional bonds: simple=18, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 327.2 milliseconds 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 612 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 65.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 16 removed outlier: 6.552A pdb=" N LEU A 5 " --> pdb=" O ILE J 6 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N LYS J 8 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG A 7 " --> pdb=" O LYS J 8 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N VAL J 10 " --> pdb=" O ARG A 7 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA A 9 " --> pdb=" O VAL J 10 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N VAL J 12 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N SER A 11 " --> pdb=" O VAL J 12 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N LYS J 14 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE A 13 " --> pdb=" O LYS J 14 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N ILE J 16 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ASN A 15 " --> pdb=" O ILE J 16 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU J 5 " --> pdb=" O ILE S 6 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N LYS S 8 " --> pdb=" O LEU J 5 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG J 7 " --> pdb=" O LYS S 8 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N VAL S 10 " --> pdb=" O ARG J 7 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA J 9 " --> pdb=" O VAL S 10 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N VAL S 12 " --> pdb=" O ALA J 9 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N SER J 11 " --> pdb=" O VAL S 12 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N LYS S 14 " --> pdb=" O SER J 11 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE J 13 " --> pdb=" O LYS S 14 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ILE S 16 " --> pdb=" O ILE J 13 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ASN J 15 " --> pdb=" O ILE S 16 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 6 through 16 removed outlier: 6.337A pdb=" N ARG B 7 " --> pdb=" O LYS K 8 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N VAL K 10 " --> pdb=" O ARG B 7 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA B 9 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N VAL K 12 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER B 11 " --> pdb=" O VAL K 12 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N LYS K 14 " --> pdb=" O SER B 11 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE B 13 " --> pdb=" O LYS K 14 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ILE K 16 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASN B 15 " --> pdb=" O ILE K 16 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARG K 7 " --> pdb=" O LYS T 8 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N VAL T 10 " --> pdb=" O ARG K 7 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA K 9 " --> pdb=" O VAL T 10 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N VAL T 12 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER K 11 " --> pdb=" O VAL T 12 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N LYS T 14 " --> pdb=" O SER K 11 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE K 13 " --> pdb=" O LYS T 14 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ILE T 16 " --> pdb=" O ILE K 13 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASN K 15 " --> pdb=" O ILE T 16 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 2 through 6 Processing sheet with id=AA4, first strand: chain 'D' and resid 5 through 16 removed outlier: 6.553A pdb=" N LEU D 5 " --> pdb=" O ILE M 6 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N LYS M 8 " --> pdb=" O LEU D 5 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ARG D 7 " --> pdb=" O LYS M 8 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N VAL M 10 " --> pdb=" O ARG D 7 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA D 9 " --> pdb=" O VAL M 10 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N VAL M 12 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N SER D 11 " --> pdb=" O VAL M 12 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N LYS M 14 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE D 13 " --> pdb=" O LYS M 14 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N ILE M 16 " --> pdb=" O ILE D 13 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASN D 15 " --> pdb=" O ILE M 16 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU M 5 " --> pdb=" O ILE V 6 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N LYS V 8 " --> pdb=" O LEU M 5 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ARG M 7 " --> pdb=" O LYS V 8 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N VAL V 10 " --> pdb=" O ARG M 7 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA M 9 " --> pdb=" O VAL V 10 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N VAL V 12 " --> pdb=" O ALA M 9 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N SER M 11 " --> pdb=" O VAL V 12 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N LYS V 14 " --> pdb=" O SER M 11 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE M 13 " --> pdb=" O LYS V 14 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ILE V 16 " --> pdb=" O ILE M 13 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASN M 15 " --> pdb=" O ILE V 16 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 6 through 16 removed outlier: 6.338A pdb=" N ARG E 7 " --> pdb=" O LYS N 8 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N VAL N 10 " --> pdb=" O ARG E 7 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ALA E 9 " --> pdb=" O VAL N 10 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N VAL N 12 " --> pdb=" O ALA E 9 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER E 11 " --> pdb=" O VAL N 12 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N LYS N 14 " --> pdb=" O SER E 11 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE E 13 " --> pdb=" O LYS N 14 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ILE N 16 " --> pdb=" O ILE E 13 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASN E 15 " --> pdb=" O ILE N 16 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ARG N 7 " --> pdb=" O LYS W 8 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N VAL W 10 " --> pdb=" O ARG N 7 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ALA N 9 " --> pdb=" O VAL W 10 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N VAL W 12 " --> pdb=" O ALA N 9 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER N 11 " --> pdb=" O VAL W 12 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N LYS W 14 " --> pdb=" O SER N 11 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE N 13 " --> pdb=" O LYS W 14 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ILE W 16 " --> pdb=" O ILE N 13 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASN N 15 " --> pdb=" O ILE W 16 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'F' and resid 2 through 6 Processing sheet with id=AA7, first strand: chain 'G' and resid 5 through 16 removed outlier: 6.551A pdb=" N LEU G 5 " --> pdb=" O ILE P 6 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N LYS P 8 " --> pdb=" O LEU G 5 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ARG G 7 " --> pdb=" O LYS P 8 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N VAL P 10 " --> pdb=" O ARG G 7 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA G 9 " --> pdb=" O VAL P 10 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N VAL P 12 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N SER G 11 " --> pdb=" O VAL P 12 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N LYS P 14 " --> pdb=" O SER G 11 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE G 13 " --> pdb=" O LYS P 14 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N ILE P 16 " --> pdb=" O ILE G 13 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ASN G 15 " --> pdb=" O ILE P 16 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU P 5 " --> pdb=" O ILE Y 6 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N LYS Y 8 " --> pdb=" O LEU P 5 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG P 7 " --> pdb=" O LYS Y 8 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N VAL Y 10 " --> pdb=" O ARG P 7 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA P 9 " --> pdb=" O VAL Y 10 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N VAL Y 12 " --> pdb=" O ALA P 9 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N SER P 11 " --> pdb=" O VAL Y 12 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N LYS Y 14 " --> pdb=" O SER P 11 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE P 13 " --> pdb=" O LYS Y 14 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N ILE Y 16 " --> pdb=" O ILE P 13 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASN P 15 " --> pdb=" O ILE Y 16 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'H' and resid 6 through 16 removed outlier: 6.337A pdb=" N ARG H 7 " --> pdb=" O LYS Q 8 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N VAL Q 10 " --> pdb=" O ARG H 7 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA H 9 " --> pdb=" O VAL Q 10 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N VAL Q 12 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER H 11 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N LYS Q 14 " --> pdb=" O SER H 11 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE H 13 " --> pdb=" O LYS Q 14 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ILE Q 16 " --> pdb=" O ILE H 13 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASN H 15 " --> pdb=" O ILE Q 16 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARG Q 7 " --> pdb=" O LYS Z 8 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N VAL Z 10 " --> pdb=" O ARG Q 7 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA Q 9 " --> pdb=" O VAL Z 10 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N VAL Z 12 " --> pdb=" O ALA Q 9 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER Q 11 " --> pdb=" O VAL Z 12 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N LYS Z 14 " --> pdb=" O SER Q 11 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE Q 13 " --> pdb=" O LYS Z 14 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ILE Z 16 " --> pdb=" O ILE Q 13 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASN Q 15 " --> pdb=" O ILE Z 16 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'I' and resid 2 through 6 24 hydrogen bonds defined for protein. 72 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.81 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 0.98: 2997 0.98 - 1.12: 0 1.12 - 1.26: 414 1.26 - 1.40: 414 1.40 - 1.54: 1692 Bond restraints: 5517 Sorted by residual: bond pdb=" N ASP T 4 " pdb=" CA ASP T 4 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.15e+00 bond pdb=" N ASP W 4 " pdb=" CA ASP W 4 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.13e+00 bond pdb=" N ASP Z 4 " pdb=" CA ASP Z 4 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 bond pdb=" N ASP N 4 " pdb=" CA ASP N 4 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 bond pdb=" N ASP K 4 " pdb=" CA ASP K 4 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 ... (remaining 5512 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 9545 0.91 - 1.81: 542 1.81 - 2.72: 20 2.72 - 3.62: 9 3.62 - 4.53: 9 Bond angle restraints: 10125 Sorted by residual: angle pdb=" N VAL F 2 " pdb=" CA VAL F 2 " pdb=" C VAL F 2 " ideal model delta sigma weight residual 109.34 106.05 3.29 2.08e+00 2.31e-01 2.49e+00 angle pdb=" N VAL R 2 " pdb=" CA VAL R 2 " pdb=" C VAL R 2 " ideal model delta sigma weight residual 109.34 106.07 3.27 2.08e+00 2.31e-01 2.47e+00 angle pdb=" N VAL a 2 " pdb=" CA VAL a 2 " pdb=" C VAL a 2 " ideal model delta sigma weight residual 109.34 106.07 3.27 2.08e+00 2.31e-01 2.47e+00 angle pdb=" N VAL I 2 " pdb=" CA VAL I 2 " pdb=" C VAL I 2 " ideal model delta sigma weight residual 109.34 106.08 3.26 2.08e+00 2.31e-01 2.46e+00 angle pdb=" N VAL U 2 " pdb=" CA VAL U 2 " pdb=" C VAL U 2 " ideal model delta sigma weight residual 109.34 106.08 3.26 2.08e+00 2.31e-01 2.45e+00 ... (remaining 10120 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.80: 2097 12.80 - 25.59: 126 25.59 - 38.39: 69 38.39 - 51.18: 30 51.18 - 63.98: 45 Dihedral angle restraints: 2367 sinusoidal: 1440 harmonic: 927 Sorted by residual: dihedral pdb=" CA LEU S 5 " pdb=" CB LEU S 5 " pdb=" CG LEU S 5 " pdb=" CD1 LEU S 5 " ideal model delta sinusoidal sigma weight residual 180.00 145.53 34.47 3 1.50e+01 4.44e-03 5.84e+00 dihedral pdb=" CA LEU G 5 " pdb=" CB LEU G 5 " pdb=" CG LEU G 5 " pdb=" CD1 LEU G 5 " ideal model delta sinusoidal sigma weight residual 180.00 145.54 34.46 3 1.50e+01 4.44e-03 5.84e+00 dihedral pdb=" CA LEU J 5 " pdb=" CB LEU J 5 " pdb=" CG LEU J 5 " pdb=" CD1 LEU J 5 " ideal model delta sinusoidal sigma weight residual 180.00 145.55 34.45 3 1.50e+01 4.44e-03 5.84e+00 ... (remaining 2364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 166 0.024 - 0.049: 121 0.049 - 0.073: 46 0.073 - 0.097: 111 0.097 - 0.121: 24 Chirality restraints: 468 Sorted by residual: chirality pdb=" CA ILE H 6 " pdb=" N ILE H 6 " pdb=" C ILE H 6 " pdb=" CB ILE H 6 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.68e-01 chirality pdb=" CA ILE T 6 " pdb=" N ILE T 6 " pdb=" C ILE T 6 " pdb=" CB ILE T 6 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.66e-01 chirality pdb=" CA ILE B 6 " pdb=" N ILE B 6 " pdb=" C ILE B 6 " pdb=" CB ILE B 6 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.64e-01 ... (remaining 465 not shown) Planarity restraints: 702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 1 " 0.002 2.00e-02 2.50e+03 3.83e-03 1.47e-01 pdb=" N VAL R 2 " -0.007 2.00e-02 2.50e+03 pdb=" CA VAL R 2 " 0.002 2.00e-02 2.50e+03 pdb=" H VAL R 2 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY I 1 " 0.002 2.00e-02 2.50e+03 3.75e-03 1.41e-01 pdb=" N VAL I 2 " -0.006 2.00e-02 2.50e+03 pdb=" CA VAL I 2 " 0.002 2.00e-02 2.50e+03 pdb=" H VAL I 2 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY a 1 " 0.002 2.00e-02 2.50e+03 3.68e-03 1.35e-01 pdb=" N VAL a 2 " -0.006 2.00e-02 2.50e+03 pdb=" CA VAL a 2 " 0.002 2.00e-02 2.50e+03 pdb=" H VAL a 2 " 0.003 2.00e-02 2.50e+03 ... (remaining 699 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.41: 2845 2.41 - 2.90: 12424 2.90 - 3.40: 10124 3.40 - 3.90: 14682 3.90 - 4.40: 19123 Nonbonded interactions: 59198 Sorted by model distance: nonbonded pdb=" HD2 ARG G 7 " pdb="HH11 ARG G 7 " model vdw 1.908 2.270 nonbonded pdb=" HD2 ARG P 7 " pdb="HH11 ARG P 7 " model vdw 1.909 2.270 nonbonded pdb=" HD2 ARG Y 7 " pdb="HH11 ARG Y 7 " model vdw 1.909 2.270 nonbonded pdb=" HD2 ARG J 7 " pdb="HH11 ARG J 7 " model vdw 1.909 2.270 nonbonded pdb=" HD2 ARG A 7 " pdb="HH11 ARG A 7 " model vdw 1.909 2.270 ... (remaining 59193 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'V' selection = chain 'Y' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'T' selection = chain 'W' selection = chain 'Z' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' selection = chain 'a' } 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: 3.640 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: 0.100 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.890 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 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 : 0.013 0.106 2538 Z= 0.957 Angle : 0.442 3.285 3348 Z= 0.231 Chirality : 0.057 0.121 468 Planarity : 0.002 0.008 387 Dihedral : 9.436 34.465 954 Min Nonbonded Distance : 2.689 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % 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: -2.64 (0.35), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.27), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG a 7 Details of bonding type rmsd hydrogen bonds : bond 0.18822 ( 24) hydrogen bonds : angle 8.71924 ( 72) covalent geometry : bond 0.00954 ( 2520) covalent geometry : angle 0.44158 ( 3348) Misc. bond : bond 0.10487 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.484 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 5.0878 time to fit residues: 103.5134 Evaluate side-chains 8 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.129377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.083894 restraints weight = 8143.944| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.16 r_work: 0.3309 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2538 Z= 0.097 Angle : 0.399 3.300 3348 Z= 0.197 Chirality : 0.061 0.127 468 Planarity : 0.002 0.006 387 Dihedral : 3.030 7.059 342 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 0.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % 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: -2.21 (0.37), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.28), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 7 Details of bonding type rmsd hydrogen bonds : bond 0.03047 ( 24) hydrogen bonds : angle 5.95889 ( 72) covalent geometry : bond 0.00219 ( 2520) covalent geometry : angle 0.39902 ( 3348) Misc. bond : bond 0.00054 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.432 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 2.2194 time to fit residues: 43.7316 Evaluate side-chains 11 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN B 15 ASN D 15 ASN E 15 ASN G 15 ASN H 15 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.124983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.078673 restraints weight = 8464.717| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.26 r_work: 0.3226 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2538 Z= 0.109 Angle : 0.361 2.604 3348 Z= 0.187 Chirality : 0.060 0.129 468 Planarity : 0.002 0.009 387 Dihedral : 2.985 6.267 342 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 0.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % 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: -2.24 (0.37), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.28), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG X 7 Details of bonding type rmsd hydrogen bonds : bond 0.03297 ( 24) hydrogen bonds : angle 5.86531 ( 72) covalent geometry : bond 0.00231 ( 2520) covalent geometry : angle 0.36112 ( 3348) Misc. bond : bond 0.00049 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.529 Fit side-chains REVERT: N 8 LYS cc_start: 0.7757 (tttt) cc_final: 0.7440 (ttmt) outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 3.1837 time to fit residues: 36.3670 Evaluate side-chains 11 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 chunk 15 optimal weight: 0.1980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.128454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.082801 restraints weight = 8481.748| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.14 r_work: 0.3250 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2538 Z= 0.098 Angle : 0.348 2.405 3348 Z= 0.180 Chirality : 0.060 0.127 468 Planarity : 0.001 0.006 387 Dihedral : 2.821 5.933 342 Min Nonbonded Distance : 2.715 Molprobity Statistics. All-atom Clashscore : 0.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.25 (0.37), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.28), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 7 Details of bonding type rmsd hydrogen bonds : bond 0.02729 ( 24) hydrogen bonds : angle 5.63573 ( 72) covalent geometry : bond 0.00209 ( 2520) covalent geometry : angle 0.34800 ( 3348) Misc. bond : bond 0.00049 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.486 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 4.5287 time to fit residues: 64.8195 Evaluate side-chains 14 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.0000 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.126095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.082171 restraints weight = 8617.037| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.12 r_work: 0.3265 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2538 Z= 0.077 Angle : 0.333 2.364 3348 Z= 0.172 Chirality : 0.061 0.125 468 Planarity : 0.001 0.007 387 Dihedral : 2.476 5.549 342 Min Nonbonded Distance : 2.717 Molprobity Statistics. All-atom Clashscore : 0.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.11 (0.38), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.29), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 7 Details of bonding type rmsd hydrogen bonds : bond 0.02449 ( 24) hydrogen bonds : angle 5.34810 ( 72) covalent geometry : bond 0.00166 ( 2520) covalent geometry : angle 0.33269 ( 3348) Misc. bond : bond 0.00035 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.485 Fit side-chains REVERT: U 4 ASP cc_start: 0.8423 (m-30) cc_final: 0.8192 (m-30) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 4.3417 time to fit residues: 84.1254 Evaluate side-chains 17 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 1 optimal weight: 0.0470 chunk 10 optimal weight: 0.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.129052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.082138 restraints weight = 8191.269| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.26 r_work: 0.3254 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.009 2538 Z= 0.093 Angle : 0.341 2.112 3348 Z= 0.177 Chirality : 0.060 0.126 468 Planarity : 0.001 0.010 387 Dihedral : 2.678 5.989 342 Min Nonbonded Distance : 2.716 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % 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: -2.18 (0.39), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.30), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 7 Details of bonding type rmsd hydrogen bonds : bond 0.02558 ( 24) hydrogen bonds : angle 5.47267 ( 72) covalent geometry : bond 0.00199 ( 2520) covalent geometry : angle 0.34080 ( 3348) Misc. bond : bond 0.00040 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.498 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 4.5880 time to fit residues: 74.9455 Evaluate side-chains 15 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 0.3980 chunk 12 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.129240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.082968 restraints weight = 8260.013| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.25 r_work: 0.3288 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.010 2538 Z= 0.067 Angle : 0.315 2.107 3348 Z= 0.164 Chirality : 0.061 0.124 468 Planarity : 0.001 0.006 387 Dihedral : 2.341 5.125 342 Min Nonbonded Distance : 2.718 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % 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: -2.05 (0.39), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.30), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG X 7 Details of bonding type rmsd hydrogen bonds : bond 0.02332 ( 24) hydrogen bonds : angle 5.24924 ( 72) covalent geometry : bond 0.00148 ( 2520) covalent geometry : angle 0.31518 ( 3348) Misc. bond : bond 0.00021 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.487 Fit side-chains REVERT: U 4 ASP cc_start: 0.8270 (m-30) cc_final: 0.8048 (m-30) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 3.7553 time to fit residues: 65.3970 Evaluate side-chains 14 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 0.0060 chunk 14 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 15 ASN G 15 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.129285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.084792 restraints weight = 8554.219| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.16 r_work: 0.3265 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.009 2538 Z= 0.087 Angle : 0.328 1.924 3348 Z= 0.172 Chirality : 0.060 0.125 468 Planarity : 0.001 0.006 387 Dihedral : 2.553 5.822 342 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 0.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % 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: -2.11 (0.39), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.30), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 7 Details of bonding type rmsd hydrogen bonds : bond 0.02494 ( 24) hydrogen bonds : angle 5.36777 ( 72) covalent geometry : bond 0.00182 ( 2520) covalent geometry : angle 0.32810 ( 3348) Misc. bond : bond 0.00036 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.467 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 4.5493 time to fit residues: 69.6200 Evaluate side-chains 15 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 0 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.129236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.083929 restraints weight = 8593.600| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.22 r_work: 0.3230 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.009 2538 Z= 0.117 Angle : 0.348 1.937 3348 Z= 0.182 Chirality : 0.059 0.126 468 Planarity : 0.001 0.007 387 Dihedral : 2.758 6.458 342 Min Nonbonded Distance : 2.682 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % 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: -2.32 (0.38), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.29), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 7 Details of bonding type rmsd hydrogen bonds : bond 0.02851 ( 24) hydrogen bonds : angle 5.56575 ( 72) covalent geometry : bond 0.00254 ( 2520) covalent geometry : angle 0.34837 ( 3348) Misc. bond : bond 0.00054 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.481 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 4.7404 time to fit residues: 77.3950 Evaluate side-chains 16 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 12 optimal weight: 0.0270 chunk 1 optimal weight: 0.8980 chunk 5 optimal weight: 0.0470 chunk 15 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.132622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.087056 restraints weight = 8360.409| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.21 r_work: 0.3317 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.012 2538 Z= 0.060 Angle : 0.310 2.015 3348 Z= 0.162 Chirality : 0.061 0.122 468 Planarity : 0.001 0.006 387 Dihedral : 2.322 5.430 342 Min Nonbonded Distance : 2.679 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % 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: -2.06 (0.39), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.30), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 7 Details of bonding type rmsd hydrogen bonds : bond 0.02156 ( 24) hydrogen bonds : angle 5.19988 ( 72) covalent geometry : bond 0.00141 ( 2520) covalent geometry : angle 0.31030 ( 3348) Misc. bond : bond 0.00015 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.408 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 4.5218 time to fit residues: 73.9547 Evaluate side-chains 15 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 0.0370 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.128331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.081590 restraints weight = 8408.620| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.32 r_work: 0.3248 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.009 2538 Z= 0.075 Angle : 0.322 1.933 3348 Z= 0.168 Chirality : 0.061 0.124 468 Planarity : 0.001 0.006 387 Dihedral : 2.432 5.722 342 Min Nonbonded Distance : 2.677 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % 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: -2.07 (0.39), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.30), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 7 Details of bonding type rmsd hydrogen bonds : bond 0.02354 ( 24) hydrogen bonds : angle 5.21400 ( 72) covalent geometry : bond 0.00160 ( 2520) covalent geometry : angle 0.32186 ( 3348) Misc. bond : bond 0.00030 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4480.11 seconds wall clock time: 77 minutes 12.30 seconds (4632.30 seconds total)