Starting phenix.real_space_refine on Sat Aug 23 00:09:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fqm_50657/08_2025/9fqm_50657.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fqm_50657/08_2025/9fqm_50657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9fqm_50657/08_2025/9fqm_50657.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fqm_50657/08_2025/9fqm_50657.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fqm_50657/08_2025/9fqm_50657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fqm_50657/08_2025/9fqm_50657.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.053 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 S 80 5.16 5 C 5552 2.51 5 N 1496 2.21 5 O 1680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8808 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1101 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 8, 'TRANS': 134} Chain: "A" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1101 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 8, 'TRANS': 134} Chain: "C" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1101 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 8, 'TRANS': 134} Chain: "D" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1101 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 8, 'TRANS': 134} Chain: "E" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1101 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 8, 'TRANS': 134} Chain: "F" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1101 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 8, 'TRANS': 134} Chain: "G" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1101 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 8, 'TRANS': 134} Chain: "H" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1101 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 8, 'TRANS': 134} Time building chain proxies: 2.35, per 1000 atoms: 0.27 Number of scatterers: 8808 At special positions: 0 Unit cell: (59.136, 78.54, 170.016, 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) S 80 16.00 O 1680 8.00 N 1496 7.00 C 5552 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=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 488.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 8 sheets defined 53.3% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'B' and resid 18 through 33 removed outlier: 4.145A pdb=" N ALA B 22 " --> pdb=" O ASP B 18 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLY B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER B 32 " --> pdb=" O TYR B 28 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 70 through 76 removed outlier: 3.812A pdb=" N LEU B 74 " --> pdb=" O THR B 70 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLN B 75 " --> pdb=" O PRO B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 90 removed outlier: 3.703A pdb=" N LYS B 80 " --> pdb=" O ASP B 76 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 90 " --> pdb=" O ALA B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 114 removed outlier: 3.568A pdb=" N ARG B 114 " --> pdb=" O PRO B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 129 removed outlier: 3.596A pdb=" N ARG B 129 " --> pdb=" O GLY B 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 126 through 129' Processing helix chain 'B' and resid 130 through 143 removed outlier: 3.801A pdb=" N ALA B 134 " --> pdb=" O GLN B 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 34 removed outlier: 4.159A pdb=" N ALA A 22 " --> pdb=" O ASP A 18 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N SER A 32 " --> pdb=" O TYR A 28 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 70 through 76 removed outlier: 3.892A pdb=" N LEU A 74 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLN A 75 " --> pdb=" O PRO A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 90 removed outlier: 3.720A pdb=" N LYS A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 114 removed outlier: 3.564A pdb=" N ARG A 114 " --> pdb=" O PRO A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 129 removed outlier: 3.609A pdb=" N ARG A 129 " --> pdb=" O GLY A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'C' and resid 18 through 34 removed outlier: 4.281A pdb=" N ALA C 22 " --> pdb=" O ASP C 18 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER C 32 " --> pdb=" O TYR C 28 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 62 Processing helix chain 'C' and resid 70 through 76 removed outlier: 3.816A pdb=" N LEU C 74 " --> pdb=" O THR C 70 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLN C 75 " --> pdb=" O PRO C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 90 removed outlier: 3.688A pdb=" N LYS C 80 " --> pdb=" O ASP C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 114 removed outlier: 3.749A pdb=" N ARG C 114 " --> pdb=" O PRO C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 129 Processing helix chain 'C' and resid 130 through 142 removed outlier: 3.796A pdb=" N ALA C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 33 removed outlier: 4.174A pdb=" N ALA D 22 " --> pdb=" O ASP D 18 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER D 32 " --> pdb=" O TYR D 28 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR D 33 " --> pdb=" O LEU D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 50 through 61 Processing helix chain 'D' and resid 70 through 76 removed outlier: 3.810A pdb=" N LEU D 74 " --> pdb=" O THR D 70 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLN D 75 " --> pdb=" O PRO D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 90 removed outlier: 3.732A pdb=" N LYS D 80 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 114 Processing helix chain 'D' and resid 125 through 129 Processing helix chain 'D' and resid 130 through 143 removed outlier: 3.786A pdb=" N ALA D 134 " --> pdb=" O GLN D 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 30 removed outlier: 4.301A pdb=" N ALA E 22 " --> pdb=" O ASP E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 Processing helix chain 'E' and resid 50 through 61 Processing helix chain 'E' and resid 76 through 90 removed outlier: 3.785A pdb=" N LYS E 80 " --> pdb=" O ASP E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 114 removed outlier: 3.816A pdb=" N ARG E 114 " --> pdb=" O PRO E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 129 Processing helix chain 'E' and resid 130 through 142 removed outlier: 3.804A pdb=" N ALA E 134 " --> pdb=" O GLN E 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 30 removed outlier: 4.212A pdb=" N ALA F 22 " --> pdb=" O ASP F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 Processing helix chain 'F' and resid 50 through 61 Processing helix chain 'F' and resid 70 through 76 removed outlier: 3.891A pdb=" N LEU F 74 " --> pdb=" O THR F 70 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLN F 75 " --> pdb=" O PRO F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 90 removed outlier: 3.738A pdb=" N LYS F 80 " --> pdb=" O ASP F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 114 removed outlier: 3.570A pdb=" N ARG F 114 " --> pdb=" O PRO F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 129 removed outlier: 3.557A pdb=" N ARG F 129 " --> pdb=" O GLY F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 143 removed outlier: 3.702A pdb=" N ALA F 134 " --> pdb=" O GLN F 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 34 removed outlier: 3.956A pdb=" N ALA G 22 " --> pdb=" O ASP G 18 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY G 31 " --> pdb=" O SER G 27 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER G 32 " --> pdb=" O TYR G 28 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR G 33 " --> pdb=" O LEU G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 45 Processing helix chain 'G' and resid 50 through 61 Processing helix chain 'G' and resid 70 through 76 removed outlier: 3.733A pdb=" N LEU G 74 " --> pdb=" O THR G 70 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLN G 75 " --> pdb=" O PRO G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 90 removed outlier: 3.746A pdb=" N LYS G 80 " --> pdb=" O ASP G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 114 removed outlier: 3.704A pdb=" N ARG G 114 " --> pdb=" O PRO G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 129 Processing helix chain 'G' and resid 130 through 143 removed outlier: 3.830A pdb=" N ALA G 134 " --> pdb=" O GLN G 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 30 removed outlier: 3.844A pdb=" N ALA H 22 " --> pdb=" O ASP H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 45 Processing helix chain 'H' and resid 50 through 61 Processing helix chain 'H' and resid 76 through 90 removed outlier: 3.557A pdb=" N LYS H 80 " --> pdb=" O ASP H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 114 removed outlier: 3.642A pdb=" N ARG H 114 " --> pdb=" O PRO H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 129 Processing helix chain 'H' and resid 130 through 143 removed outlier: 3.817A pdb=" N ALA H 134 " --> pdb=" O GLN H 130 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 38 through 39 removed outlier: 6.205A pdb=" N VAL B 10 " --> pdb=" O PHE B 39 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N CYS B 11 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU B 68 " --> pdb=" O CYS B 11 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N CYS B 13 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 13 Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.853A pdb=" N ARG C 65 " --> pdb=" O ILE C 98 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU C 100 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU C 67 " --> pdb=" O LEU C 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 38 through 39 removed outlier: 6.554A pdb=" N VAL D 10 " --> pdb=" O PHE D 39 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG D 65 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N LEU D 100 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU D 67 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 10 through 13 Processing sheet with id=AA6, first strand: chain 'F' and resid 38 through 39 removed outlier: 6.471A pdb=" N VAL F 10 " --> pdb=" O PHE F 39 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ARG F 65 " --> pdb=" O ILE F 98 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LEU F 100 " --> pdb=" O ARG F 65 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU F 67 " --> pdb=" O LEU F 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AA8, first strand: chain 'H' and resid 38 through 39 removed outlier: 6.544A pdb=" N VAL H 10 " --> pdb=" O PHE H 39 " (cutoff:3.500A) 368 hydrogen bonds defined for protein. 1047 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: 1.33 Time building geometry restraints manager: 0.97 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: 2912 1.34 - 1.46: 1970 1.46 - 1.58: 4014 1.58 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 9000 Sorted by residual: bond pdb=" CB PRO E 47 " pdb=" CG PRO E 47 " ideal model delta sigma weight residual 1.492 1.563 -0.071 5.00e-02 4.00e+02 2.01e+00 bond pdb=" CB PRO F 47 " pdb=" CG PRO F 47 " ideal model delta sigma weight residual 1.492 1.544 -0.052 5.00e-02 4.00e+02 1.07e+00 bond pdb=" CB PRO D 47 " pdb=" CG PRO D 47 " ideal model delta sigma weight residual 1.492 1.540 -0.048 5.00e-02 4.00e+02 9.12e-01 bond pdb=" C ILE H 98 " pdb=" O ILE H 98 " ideal model delta sigma weight residual 1.232 1.239 -0.008 1.01e-02 9.80e+03 5.52e-01 bond pdb=" N GLY G 123 " pdb=" CA GLY G 123 " ideal model delta sigma weight residual 1.434 1.443 -0.009 1.22e-02 6.72e+03 5.47e-01 ... (remaining 8995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 11716 1.20 - 2.39: 384 2.39 - 3.59: 81 3.59 - 4.78: 30 4.78 - 5.98: 5 Bond angle restraints: 12216 Sorted by residual: angle pdb=" N SER G 35 " pdb=" CA SER G 35 " pdb=" C SER G 35 " ideal model delta sigma weight residual 114.56 110.29 4.27 1.27e+00 6.20e-01 1.13e+01 angle pdb=" N SER C 35 " pdb=" CA SER C 35 " pdb=" C SER C 35 " ideal model delta sigma weight residual 114.56 110.51 4.05 1.27e+00 6.20e-01 1.02e+01 angle pdb=" CA SER G 35 " pdb=" C SER G 35 " pdb=" N LEU G 36 " ideal model delta sigma weight residual 119.26 116.60 2.66 1.14e+00 7.69e-01 5.43e+00 angle pdb=" CA SER C 35 " pdb=" C SER C 35 " pdb=" N LEU C 36 " ideal model delta sigma weight residual 119.26 116.67 2.59 1.14e+00 7.69e-01 5.15e+00 angle pdb=" N ASP E 44 " pdb=" CA ASP E 44 " pdb=" C ASP E 44 " ideal model delta sigma weight residual 110.80 115.22 -4.42 2.13e+00 2.20e-01 4.31e+00 ... (remaining 12211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 4798 15.07 - 30.13: 438 30.13 - 45.20: 130 45.20 - 60.27: 19 60.27 - 75.34: 31 Dihedral angle restraints: 5416 sinusoidal: 2112 harmonic: 3304 Sorted by residual: dihedral pdb=" CA ARG H 129 " pdb=" C ARG H 129 " pdb=" N GLN H 130 " pdb=" CA GLN H 130 " ideal model delta harmonic sigma weight residual 180.00 163.63 16.37 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA MET D 116 " pdb=" C MET D 116 " pdb=" N TYR D 117 " pdb=" CA TYR D 117 " ideal model delta harmonic sigma weight residual 180.00 163.97 16.03 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA LYS F 132 " pdb=" CB LYS F 132 " pdb=" CG LYS F 132 " pdb=" CD LYS F 132 " ideal model delta sinusoidal sigma weight residual -60.00 -111.56 51.56 3 1.50e+01 4.44e-03 9.03e+00 ... (remaining 5413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 700 0.023 - 0.046: 374 0.046 - 0.069: 152 0.069 - 0.091: 78 0.091 - 0.114: 48 Chirality restraints: 1352 Sorted by residual: chirality pdb=" CA ILE F 98 " pdb=" N ILE F 98 " pdb=" C ILE F 98 " pdb=" CB ILE F 98 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.27e-01 chirality pdb=" CA ILE E 98 " pdb=" N ILE E 98 " pdb=" C ILE E 98 " pdb=" CB ILE E 98 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 3.10e-01 chirality pdb=" CA ILE B 98 " pdb=" N ILE B 98 " pdb=" C ILE B 98 " pdb=" CB ILE B 98 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.90e-01 ... (remaining 1349 not shown) Planarity restraints: 1584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 46 " -0.064 5.00e-02 4.00e+02 9.63e-02 1.49e+01 pdb=" N PRO C 47 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO C 47 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 47 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR G 109 " -0.033 5.00e-02 4.00e+02 5.07e-02 4.12e+00 pdb=" N PRO G 110 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO G 110 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO G 110 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 76 " 0.030 5.00e-02 4.00e+02 4.61e-02 3.39e+00 pdb=" N PRO E 77 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO E 77 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 77 " 0.026 5.00e-02 4.00e+02 ... (remaining 1581 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1654 2.77 - 3.30: 8503 3.30 - 3.84: 14175 3.84 - 4.37: 16158 4.37 - 4.90: 28284 Nonbonded interactions: 68774 Sorted by model distance: nonbonded pdb=" OG SER G 15 " pdb=" OD1 ASP G 18 " model vdw 2.240 3.040 nonbonded pdb=" OG SER H 15 " pdb=" OD1 ASP H 18 " model vdw 2.248 3.040 nonbonded pdb=" OG SER E 15 " pdb=" OD1 ASP E 18 " model vdw 2.271 3.040 nonbonded pdb=" OG SER F 15 " pdb=" OD1 ASP F 18 " model vdw 2.272 3.040 nonbonded pdb=" O LYS B 6 " pdb=" NH2 ARG B 37 " model vdw 2.275 3.120 ... (remaining 68769 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 1.850 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: 0.020 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.640 Find NCS groups from input model: 0.140 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5310 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 0.071 9000 Z= 0.114 Angle : 0.561 5.981 12216 Z= 0.291 Chirality : 0.038 0.114 1352 Planarity : 0.006 0.096 1584 Dihedral : 14.441 75.336 3304 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.26), residues: 1128 helix: 1.19 (0.25), residues: 464 sheet: 0.01 (0.43), residues: 168 loop : 0.50 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 37 TYR 0.017 0.002 TYR D 138 PHE 0.008 0.001 PHE H 73 TRP 0.006 0.001 TRP F 4 HIS 0.003 0.001 HIS B 14 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9000) covalent geometry : angle 0.56100 (12216) hydrogen bonds : bond 0.14412 ( 368) hydrogen bonds : angle 5.86176 ( 1047) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 TYR cc_start: 0.6176 (m-80) cc_final: 0.5958 (m-10) REVERT: E 3 ARG cc_start: 0.1302 (ttp80) cc_final: -0.0479 (ttp80) REVERT: G 36 LEU cc_start: 0.2998 (mm) cc_final: 0.2234 (tp) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.0821 time to fit residues: 27.0829 Evaluate side-chains 105 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.0050 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.0270 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.5254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS C 14 HIS D 82 GLN D 140 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.201461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.180154 restraints weight = 12035.755| |-----------------------------------------------------------------------------| r_work (start): 0.4332 rms_B_bonded: 3.05 r_work: 0.4207 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6045 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9000 Z= 0.120 Angle : 0.628 8.812 12216 Z= 0.310 Chirality : 0.041 0.124 1352 Planarity : 0.006 0.050 1584 Dihedral : 4.202 14.923 1264 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.12 % Allowed : 10.62 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.26), residues: 1128 helix: 1.34 (0.24), residues: 472 sheet: -0.08 (0.41), residues: 168 loop : 0.79 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 65 TYR 0.012 0.001 TYR A 109 PHE 0.014 0.002 PHE B 39 TRP 0.040 0.001 TRP C 4 HIS 0.004 0.001 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9000) covalent geometry : angle 0.62830 (12216) hydrogen bonds : bond 0.03108 ( 368) hydrogen bonds : angle 4.24155 ( 1047) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 130 GLN cc_start: 0.4713 (mm-40) cc_final: 0.4245 (mm-40) REVERT: E 3 ARG cc_start: 0.0935 (ttp80) cc_final: -0.0694 (ttp80) REVERT: G 6 LYS cc_start: 0.6104 (tppp) cc_final: 0.5864 (ttpt) outliers start: 30 outliers final: 21 residues processed: 153 average time/residue: 0.0815 time to fit residues: 17.5413 Evaluate side-chains 124 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain H residue 133 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 32 optimal weight: 0.0060 chunk 106 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 chunk 84 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 overall best weight: 1.2802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.192029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.170818 restraints weight = 11885.790| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 3.04 r_work: 0.4107 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.6223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9000 Z= 0.177 Angle : 0.670 6.732 12216 Z= 0.347 Chirality : 0.043 0.166 1352 Planarity : 0.006 0.045 1584 Dihedral : 4.386 14.766 1264 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.10 % Allowed : 11.46 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.26), residues: 1128 helix: 1.18 (0.24), residues: 472 sheet: -0.62 (0.42), residues: 168 loop : 0.60 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 37 TYR 0.019 0.002 TYR F 109 PHE 0.013 0.002 PHE D 73 TRP 0.027 0.002 TRP C 4 HIS 0.003 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 9000) covalent geometry : angle 0.67033 (12216) hydrogen bonds : bond 0.04037 ( 368) hydrogen bonds : angle 4.20052 ( 1047) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 190 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 136 MET cc_start: 0.6738 (mmp) cc_final: 0.6454 (mmm) REVERT: C 76 ASP cc_start: 0.8803 (t0) cc_final: 0.8568 (t0) REVERT: C 88 THR cc_start: 0.8830 (m) cc_final: 0.8578 (p) REVERT: C 133 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.7971 (mp0) REVERT: D 3 ARG cc_start: 0.4211 (tmm160) cc_final: 0.0237 (mmm160) REVERT: F 133 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7968 (mp0) REVERT: G 83 MET cc_start: 0.8716 (ttp) cc_final: 0.8499 (ttt) REVERT: H 25 LEU cc_start: 0.5630 (OUTLIER) cc_final: 0.5242 (tp) outliers start: 49 outliers final: 25 residues processed: 221 average time/residue: 0.0895 time to fit residues: 27.7164 Evaluate side-chains 175 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 131 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 GLN D 140 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.188583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.166623 restraints weight = 12158.894| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 3.12 r_work: 0.4060 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.7213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9000 Z= 0.159 Angle : 0.624 7.181 12216 Z= 0.321 Chirality : 0.042 0.168 1352 Planarity : 0.006 0.048 1584 Dihedral : 4.298 14.886 1264 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 6.15 % Allowed : 13.96 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.26), residues: 1128 helix: 1.30 (0.24), residues: 472 sheet: -0.06 (0.47), residues: 136 loop : 0.50 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 129 TYR 0.016 0.002 TYR H 109 PHE 0.016 0.002 PHE H 73 TRP 0.013 0.002 TRP G 4 HIS 0.002 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 9000) covalent geometry : angle 0.62435 (12216) hydrogen bonds : bond 0.03295 ( 368) hydrogen bonds : angle 4.10631 ( 1047) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 191 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 LEU cc_start: 0.6114 (OUTLIER) cc_final: 0.5436 (tp) REVERT: B 36 LEU cc_start: 0.2573 (OUTLIER) cc_final: 0.2323 (mp) REVERT: A 25 LEU cc_start: 0.5478 (OUTLIER) cc_final: 0.5265 (tp) REVERT: C 25 LEU cc_start: 0.5936 (OUTLIER) cc_final: 0.5351 (tp) REVERT: C 136 MET cc_start: 0.7351 (mmp) cc_final: 0.7034 (mmm) REVERT: D 3 ARG cc_start: 0.4675 (tmm160) cc_final: 0.0589 (mmm160) REVERT: D 133 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.7866 (mp0) REVERT: E 25 LEU cc_start: 0.6149 (OUTLIER) cc_final: 0.5687 (tp) REVERT: F 25 LEU cc_start: 0.6152 (OUTLIER) cc_final: 0.5845 (tp) REVERT: H 25 LEU cc_start: 0.5755 (OUTLIER) cc_final: 0.5382 (tp) REVERT: H 59 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7995 (mm) REVERT: H 136 MET cc_start: 0.7405 (mmp) cc_final: 0.7171 (mmm) outliers start: 59 outliers final: 28 residues processed: 234 average time/residue: 0.1003 time to fit residues: 31.7550 Evaluate side-chains 196 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 159 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 133 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 46 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 60 optimal weight: 0.0040 chunk 73 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 HIS G 14 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.187352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.165195 restraints weight = 12290.220| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 3.13 r_work: 0.4048 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.7791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9000 Z= 0.132 Angle : 0.606 8.638 12216 Z= 0.308 Chirality : 0.041 0.165 1352 Planarity : 0.006 0.048 1584 Dihedral : 4.148 15.530 1264 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.69 % Allowed : 15.42 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.26), residues: 1128 helix: 1.50 (0.24), residues: 472 sheet: -0.06 (0.48), residues: 136 loop : 0.48 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 129 TYR 0.017 0.002 TYR G 138 PHE 0.011 0.001 PHE A 73 TRP 0.008 0.001 TRP C 4 HIS 0.002 0.000 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9000) covalent geometry : angle 0.60562 (12216) hydrogen bonds : bond 0.03072 ( 368) hydrogen bonds : angle 4.07219 ( 1047) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 185 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 LEU cc_start: 0.5920 (OUTLIER) cc_final: 0.5311 (tp) REVERT: B 56 CYS cc_start: 0.7837 (t) cc_final: 0.7593 (m) REVERT: B 76 ASP cc_start: 0.8746 (t0) cc_final: 0.8341 (t0) REVERT: B 130 GLN cc_start: 0.5644 (tp40) cc_final: 0.5208 (mm-40) REVERT: B 133 GLU cc_start: 0.8363 (pt0) cc_final: 0.7883 (mp0) REVERT: A 25 LEU cc_start: 0.5382 (OUTLIER) cc_final: 0.5172 (tp) REVERT: A 57 GLN cc_start: 0.8283 (tm-30) cc_final: 0.8035 (tp-100) REVERT: C 25 LEU cc_start: 0.5891 (OUTLIER) cc_final: 0.5355 (tp) REVERT: C 76 ASP cc_start: 0.8824 (t0) cc_final: 0.8623 (t0) REVERT: D 3 ARG cc_start: 0.4708 (tmm160) cc_final: 0.0731 (mmm160) REVERT: D 136 MET cc_start: 0.7266 (mmp) cc_final: 0.6977 (mmm) REVERT: E 25 LEU cc_start: 0.6101 (OUTLIER) cc_final: 0.5706 (tp) REVERT: E 57 GLN cc_start: 0.8429 (tp40) cc_final: 0.8182 (tp-100) REVERT: F 18 ASP cc_start: 0.5876 (m-30) cc_final: 0.5206 (p0) REVERT: F 133 GLU cc_start: 0.8327 (pt0) cc_final: 0.7883 (mp0) REVERT: H 25 LEU cc_start: 0.5757 (OUTLIER) cc_final: 0.5470 (tp) REVERT: H 59 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8038 (mm) outliers start: 45 outliers final: 21 residues processed: 220 average time/residue: 0.1103 time to fit residues: 32.2730 Evaluate side-chains 186 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 66 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 87 optimal weight: 0.2980 chunk 78 optimal weight: 0.7980 chunk 108 optimal weight: 0.3980 chunk 94 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 4 optimal weight: 0.0040 chunk 18 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.189228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.167305 restraints weight = 12347.976| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 3.11 r_work: 0.4058 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.8052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9000 Z= 0.111 Angle : 0.583 7.650 12216 Z= 0.293 Chirality : 0.039 0.130 1352 Planarity : 0.005 0.049 1584 Dihedral : 3.978 14.824 1264 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.85 % Allowed : 16.88 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.26), residues: 1128 helix: 1.78 (0.25), residues: 472 sheet: -0.02 (0.48), residues: 136 loop : 0.49 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 37 TYR 0.014 0.001 TYR G 138 PHE 0.012 0.001 PHE C 73 TRP 0.007 0.001 TRP B 4 HIS 0.002 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9000) covalent geometry : angle 0.58316 (12216) hydrogen bonds : bond 0.02670 ( 368) hydrogen bonds : angle 4.03799 ( 1047) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 185 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 LEU cc_start: 0.5923 (OUTLIER) cc_final: 0.5422 (tp) REVERT: B 76 ASP cc_start: 0.8789 (t0) cc_final: 0.8438 (t0) REVERT: B 88 THR cc_start: 0.8817 (m) cc_final: 0.8570 (p) REVERT: B 133 GLU cc_start: 0.8271 (pt0) cc_final: 0.7840 (mp0) REVERT: B 136 MET cc_start: 0.6877 (mmp) cc_final: 0.6564 (mmm) REVERT: A 57 GLN cc_start: 0.8215 (tm-30) cc_final: 0.8003 (tp-100) REVERT: C 25 LEU cc_start: 0.5816 (OUTLIER) cc_final: 0.5385 (tp) REVERT: C 76 ASP cc_start: 0.8898 (t0) cc_final: 0.8685 (t0) REVERT: D 3 ARG cc_start: 0.4757 (tmm160) cc_final: 0.0938 (mmm160) REVERT: D 38 CYS cc_start: 0.6494 (m) cc_final: 0.6214 (t) REVERT: E 25 LEU cc_start: 0.5881 (OUTLIER) cc_final: 0.5559 (tp) REVERT: E 57 GLN cc_start: 0.8383 (tp40) cc_final: 0.8153 (tp-100) REVERT: E 133 GLU cc_start: 0.8475 (pt0) cc_final: 0.7986 (mp0) REVERT: F 18 ASP cc_start: 0.5621 (m-30) cc_final: 0.5129 (p0) REVERT: G 133 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8197 (mp0) REVERT: G 136 MET cc_start: 0.6957 (mmp) cc_final: 0.6648 (mmm) REVERT: H 59 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7974 (mm) REVERT: H 130 GLN cc_start: 0.5388 (tp40) cc_final: 0.5034 (mm-40) REVERT: H 133 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8065 (mp0) outliers start: 37 outliers final: 21 residues processed: 211 average time/residue: 0.1105 time to fit residues: 31.1188 Evaluate side-chains 190 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain H residue 133 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 53 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.187147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.169609 restraints weight = 12401.734| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 2.32 r_work: 0.4093 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.8498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9000 Z= 0.139 Angle : 0.637 6.882 12216 Z= 0.324 Chirality : 0.041 0.122 1352 Planarity : 0.006 0.056 1584 Dihedral : 4.021 15.707 1264 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.96 % Allowed : 18.44 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.26), residues: 1128 helix: 1.68 (0.25), residues: 480 sheet: -0.03 (0.49), residues: 136 loop : 0.54 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 137 TYR 0.013 0.002 TYR G 138 PHE 0.011 0.001 PHE H 73 TRP 0.007 0.001 TRP B 4 HIS 0.001 0.000 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9000) covalent geometry : angle 0.63721 (12216) hydrogen bonds : bond 0.03070 ( 368) hydrogen bonds : angle 4.03837 ( 1047) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 LEU cc_start: 0.5856 (OUTLIER) cc_final: 0.5448 (tp) REVERT: A 18 ASP cc_start: 0.5751 (p0) cc_final: 0.5405 (p0) REVERT: C 25 LEU cc_start: 0.5794 (OUTLIER) cc_final: 0.5405 (tp) REVERT: D 3 ARG cc_start: 0.4755 (tmm160) cc_final: 0.1163 (mmm160) REVERT: E 25 LEU cc_start: 0.6013 (OUTLIER) cc_final: 0.5713 (tp) REVERT: E 57 GLN cc_start: 0.8481 (tp40) cc_final: 0.8272 (tp-100) REVERT: G 6 LYS cc_start: 0.6046 (tppp) cc_final: 0.5546 (tppp) REVERT: G 25 LEU cc_start: 0.5974 (OUTLIER) cc_final: 0.5751 (tp) REVERT: H 36 LEU cc_start: 0.2348 (OUTLIER) cc_final: 0.2133 (mp) REVERT: H 59 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8265 (mm) REVERT: H 130 GLN cc_start: 0.5171 (tp40) cc_final: 0.4945 (mm-40) outliers start: 38 outliers final: 23 residues processed: 201 average time/residue: 0.1157 time to fit residues: 30.8038 Evaluate side-chains 182 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 116 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 59 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 110 optimal weight: 0.0370 chunk 97 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.187099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.170111 restraints weight = 12329.975| |-----------------------------------------------------------------------------| r_work (start): 0.4222 rms_B_bonded: 2.26 r_work: 0.4100 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.8772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9000 Z= 0.131 Angle : 0.633 7.668 12216 Z= 0.324 Chirality : 0.041 0.153 1352 Planarity : 0.005 0.050 1584 Dihedral : 3.973 16.496 1264 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.65 % Allowed : 19.06 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.26), residues: 1128 helix: 1.81 (0.25), residues: 472 sheet: -0.04 (0.49), residues: 136 loop : 0.41 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 129 TYR 0.017 0.002 TYR G 138 PHE 0.010 0.001 PHE A 73 TRP 0.006 0.001 TRP B 4 HIS 0.002 0.000 HIS H 63 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9000) covalent geometry : angle 0.63335 (12216) hydrogen bonds : bond 0.03013 ( 368) hydrogen bonds : angle 4.00104 ( 1047) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 LEU cc_start: 0.5806 (OUTLIER) cc_final: 0.5450 (tp) REVERT: A 46 THR cc_start: 0.6743 (p) cc_final: 0.6486 (p) REVERT: C 25 LEU cc_start: 0.5728 (OUTLIER) cc_final: 0.5424 (tp) REVERT: D 3 ARG cc_start: 0.4823 (tmm160) cc_final: 0.1345 (mmm160) REVERT: D 101 LEU cc_start: 0.6751 (mm) cc_final: 0.6289 (tt) REVERT: E 25 LEU cc_start: 0.5800 (OUTLIER) cc_final: 0.5568 (tp) REVERT: E 136 MET cc_start: 0.6830 (mmm) cc_final: 0.6565 (mmp) REVERT: F 129 ARG cc_start: 0.4881 (mpt180) cc_final: 0.4596 (mpp-170) REVERT: G 6 LYS cc_start: 0.6154 (tppp) cc_final: 0.5660 (tppp) REVERT: H 59 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8258 (mm) REVERT: H 133 GLU cc_start: 0.8350 (mp0) cc_final: 0.8140 (mp0) outliers start: 35 outliers final: 21 residues processed: 195 average time/residue: 0.1170 time to fit residues: 30.2544 Evaluate side-chains 182 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 116 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 82 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 104 optimal weight: 0.1980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.183784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.166454 restraints weight = 12289.374| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 2.28 r_work: 0.4060 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.9404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9000 Z= 0.194 Angle : 0.723 7.911 12216 Z= 0.371 Chirality : 0.045 0.181 1352 Planarity : 0.006 0.052 1584 Dihedral : 4.373 15.419 1264 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.12 % Allowed : 20.21 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.26), residues: 1128 helix: 1.42 (0.24), residues: 472 sheet: -0.47 (0.47), residues: 136 loop : 0.25 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 37 TYR 0.021 0.002 TYR F 109 PHE 0.015 0.002 PHE H 73 TRP 0.010 0.002 TRP E 78 HIS 0.002 0.001 HIS B 14 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 9000) covalent geometry : angle 0.72349 (12216) hydrogen bonds : bond 0.03943 ( 368) hydrogen bonds : angle 4.21659 ( 1047) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: B 25 LEU cc_start: 0.5937 (OUTLIER) cc_final: 0.5482 (tp) REVERT: A 18 ASP cc_start: 0.5777 (p0) cc_final: 0.5323 (p0) REVERT: C 25 LEU cc_start: 0.5813 (OUTLIER) cc_final: 0.5364 (tp) REVERT: D 3 ARG cc_start: 0.5384 (tmm160) cc_final: 0.0914 (ptm160) REVERT: D 101 LEU cc_start: 0.6821 (mm) cc_final: 0.6398 (tt) REVERT: E 25 LEU cc_start: 0.6106 (OUTLIER) cc_final: 0.5617 (tp) REVERT: E 136 MET cc_start: 0.6874 (mmm) cc_final: 0.6557 (mmp) REVERT: H 18 ASP cc_start: 0.6700 (p0) cc_final: 0.6495 (p0) REVERT: H 57 GLN cc_start: 0.8635 (tp40) cc_final: 0.8345 (tp-100) REVERT: H 59 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8181 (mm) outliers start: 30 outliers final: 17 residues processed: 205 average time/residue: 0.1345 time to fit residues: 35.3315 Evaluate side-chains 184 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 116 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.184984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.168014 restraints weight = 12459.326| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 2.25 r_work: 0.4063 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.9699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9000 Z= 0.143 Angle : 0.679 7.234 12216 Z= 0.342 Chirality : 0.043 0.264 1352 Planarity : 0.005 0.053 1584 Dihedral : 4.181 17.121 1264 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.29 % Allowed : 21.35 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.26), residues: 1128 helix: 1.49 (0.25), residues: 480 sheet: -0.46 (0.48), residues: 136 loop : 0.39 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 137 TYR 0.018 0.002 TYR G 138 PHE 0.010 0.001 PHE A 73 TRP 0.007 0.001 TRP E 78 HIS 0.002 0.000 HIS E 14 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 9000) covalent geometry : angle 0.67856 (12216) hydrogen bonds : bond 0.03307 ( 368) hydrogen bonds : angle 4.15177 ( 1047) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 129 ARG cc_start: 0.6023 (mpt180) cc_final: 0.5793 (mpt180) REVERT: C 25 LEU cc_start: 0.5732 (OUTLIER) cc_final: 0.5375 (tp) REVERT: D 3 ARG cc_start: 0.5102 (tmm160) cc_final: 0.1176 (ptm160) REVERT: D 101 LEU cc_start: 0.6671 (mm) cc_final: 0.6304 (tt) REVERT: E 25 LEU cc_start: 0.5942 (OUTLIER) cc_final: 0.5741 (tp) REVERT: H 57 GLN cc_start: 0.8552 (tp40) cc_final: 0.8253 (tp-100) outliers start: 22 outliers final: 15 residues processed: 193 average time/residue: 0.1173 time to fit residues: 29.9929 Evaluate side-chains 180 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 79 CYS Chi-restraints excluded: chain H residue 116 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 60 optimal weight: 1.9990 chunk 54 optimal weight: 0.0570 chunk 55 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 23 optimal weight: 0.0570 chunk 105 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 22 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 56 optimal weight: 7.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.187118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.170234 restraints weight = 12274.596| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 2.25 r_work: 0.4090 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.9790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9000 Z= 0.131 Angle : 0.678 8.440 12216 Z= 0.339 Chirality : 0.041 0.204 1352 Planarity : 0.005 0.055 1584 Dihedral : 4.016 18.080 1264 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.77 % Allowed : 22.19 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.27), residues: 1128 helix: 1.13 (0.25), residues: 528 sheet: -0.44 (0.48), residues: 136 loop : 0.61 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 137 TYR 0.015 0.001 TYR G 138 PHE 0.011 0.001 PHE A 73 TRP 0.007 0.001 TRP C 4 HIS 0.002 0.001 HIS H 63 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9000) covalent geometry : angle 0.67824 (12216) hydrogen bonds : bond 0.02957 ( 368) hydrogen bonds : angle 4.09760 ( 1047) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1824.81 seconds wall clock time: 32 minutes 25.55 seconds (1945.55 seconds total)