Starting phenix.real_space_refine on Sat Jul 26 16:23:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fqm_50657/07_2025/9fqm_50657.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fqm_50657/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9fqm_50657/07_2025/9fqm_50657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fqm_50657/07_2025/9fqm_50657.map" model { file = "/net/cci-nas-00/data/ceres_data/9fqm_50657/07_2025/9fqm_50657.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fqm_50657/07_2025/9fqm_50657.cif" } resolution = 3.3 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= 0.004 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.22, per 1000 atoms: 0.71 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: 2.42 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.99 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: 2.11 Time building geometry restraints manager: 2.85 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: 0.02 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: 1.420 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: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.420 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.860 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (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 TRP 0.006 0.001 TRP F 4 HIS 0.003 0.001 HIS B 14 PHE 0.008 0.001 PHE H 73 TYR 0.017 0.002 TYR D 138 ARG 0.004 0.000 ARG G 37 Details of bonding type rmsd hydrogen bonds : bond 0.14412 ( 368) hydrogen bonds : angle 5.86176 ( 1047) covalent geometry : bond 0.00257 ( 9000) covalent geometry : angle 0.56100 (12216) *********************** 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 : 1.307 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: 0.1950 time to fit residues: 63.2918 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 : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.3980 chunk 65 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS B 41 GLN ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4544 r_free = 0.4544 target = 0.199962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.178815 restraints weight = 11884.951| |-----------------------------------------------------------------------------| r_work (start): 0.4317 rms_B_bonded: 3.01 r_work: 0.4194 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6173 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9000 Z= 0.139 Angle : 0.653 9.203 12216 Z= 0.323 Chirality : 0.042 0.126 1352 Planarity : 0.006 0.051 1584 Dihedral : 4.251 15.156 1264 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.33 % Allowed : 11.35 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.26), residues: 1128 helix: 1.32 (0.24), residues: 472 sheet: -0.12 (0.41), residues: 168 loop : 0.80 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 4 HIS 0.004 0.001 HIS A 14 PHE 0.014 0.002 PHE B 39 TYR 0.014 0.002 TYR D 109 ARG 0.007 0.001 ARG B 65 Details of bonding type rmsd hydrogen bonds : bond 0.03234 ( 368) hydrogen bonds : angle 4.22994 ( 1047) covalent geometry : bond 0.00315 ( 9000) covalent geometry : angle 0.65282 (12216) *********************** 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 164 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.938 Fit side-chains REVERT: B 8 TYR cc_start: 0.6540 (m-80) cc_final: 0.6245 (m-10) REVERT: A 130 GLN cc_start: 0.4775 (mm-40) cc_final: 0.4269 (mm-40) REVERT: A 133 GLU cc_start: 0.8429 (tt0) cc_final: 0.8224 (tt0) REVERT: E 3 ARG cc_start: 0.1068 (ttp80) cc_final: -0.0560 (ttp80) outliers start: 32 outliers final: 23 residues processed: 155 average time/residue: 0.2081 time to fit residues: 44.6947 Evaluate side-chains 120 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 96 CYS 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 66 VAL 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 68 optimal weight: 7.9990 chunk 21 optimal weight: 0.0070 chunk 23 optimal weight: 0.0770 chunk 19 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 overall best weight: 1.0160 ------------------------------------------------------------------------------- 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 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 = 0.4463 r_free = 0.4463 target = 0.192068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.168732 restraints weight = 12145.504| |-----------------------------------------------------------------------------| r_work (start): 0.4209 rms_B_bonded: 3.40 r_work: 0.4063 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.6076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9000 Z= 0.152 Angle : 0.630 6.654 12216 Z= 0.322 Chirality : 0.041 0.165 1352 Planarity : 0.006 0.046 1584 Dihedral : 4.170 15.214 1264 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 5.42 % Allowed : 11.67 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.26), residues: 1128 helix: 1.30 (0.24), residues: 472 sheet: -0.54 (0.42), residues: 168 loop : 0.64 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 4 HIS 0.003 0.001 HIS B 63 PHE 0.012 0.002 PHE D 73 TYR 0.015 0.002 TYR H 109 ARG 0.006 0.001 ARG E 37 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 368) hydrogen bonds : angle 4.05834 ( 1047) covalent geometry : bond 0.00364 ( 9000) covalent geometry : angle 0.62970 (12216) *********************** 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 236 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 184 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.5706 (OUTLIER) cc_final: 0.5504 (tp) REVERT: A 54 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7086 (mm-30) REVERT: A 130 GLN cc_start: 0.5759 (mm-40) cc_final: 0.5485 (mm110) REVERT: C 25 LEU cc_start: 0.6019 (OUTLIER) cc_final: 0.5410 (tp) REVERT: C 54 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7579 (mm-30) REVERT: C 76 ASP cc_start: 0.8692 (t0) cc_final: 0.8433 (t0) REVERT: C 88 THR cc_start: 0.8820 (m) cc_final: 0.8608 (p) REVERT: C 133 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: D 3 ARG cc_start: 0.4214 (tmm160) cc_final: 0.0314 (mmm160) REVERT: D 25 LEU cc_start: 0.5686 (OUTLIER) cc_final: 0.5411 (tp) REVERT: F 76 ASP cc_start: 0.8822 (t0) cc_final: 0.8396 (t0) REVERT: F 133 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: H 25 LEU cc_start: 0.5638 (OUTLIER) cc_final: 0.5240 (tp) outliers start: 52 outliers final: 23 residues processed: 219 average time/residue: 0.2020 time to fit residues: 61.3434 Evaluate side-chains 171 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 25 LEU 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 133 GLU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 133 GLU 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 F residue 10 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 100 LEU 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 77 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 95 optimal weight: 0.0030 chunk 11 optimal weight: 0.8980 overall best weight: 0.9592 ------------------------------------------------------------------------------- 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 14 HIS D 140 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.190410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.168071 restraints weight = 12160.293| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 3.14 r_work: 0.4063 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.6920 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= 0.136 Angle : 0.595 7.235 12216 Z= 0.304 Chirality : 0.041 0.179 1352 Planarity : 0.005 0.048 1584 Dihedral : 4.112 13.724 1264 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.21 % Allowed : 15.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.26), residues: 1128 helix: 1.51 (0.24), residues: 472 sheet: 0.09 (0.48), residues: 136 loop : 0.56 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 4 HIS 0.002 0.001 HIS A 14 PHE 0.015 0.002 PHE H 73 TYR 0.015 0.002 TYR A 138 ARG 0.020 0.001 ARG G 129 Details of bonding type rmsd hydrogen bonds : bond 0.02990 ( 368) hydrogen bonds : angle 3.97471 ( 1047) covalent geometry : bond 0.00336 ( 9000) covalent geometry : angle 0.59486 (12216) *********************** 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 227 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 177 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 25 LEU cc_start: 0.6151 (OUTLIER) cc_final: 0.5484 (tp) REVERT: B 76 ASP cc_start: 0.8820 (t0) cc_final: 0.8220 (t0) REVERT: C 25 LEU cc_start: 0.6051 (OUTLIER) cc_final: 0.5479 (tp) REVERT: C 136 MET cc_start: 0.7361 (mmp) cc_final: 0.7105 (mmm) REVERT: D 3 ARG cc_start: 0.4402 (tmm160) cc_final: 0.0604 (mmm160) REVERT: D 25 LEU cc_start: 0.5748 (OUTLIER) cc_final: 0.5535 (tp) REVERT: D 133 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7823 (mp0) REVERT: E 25 LEU cc_start: 0.5925 (OUTLIER) cc_final: 0.5470 (tp) REVERT: F 18 ASP cc_start: 0.5661 (m-30) cc_final: 0.5106 (p0) REVERT: F 25 LEU cc_start: 0.6097 (OUTLIER) cc_final: 0.5830 (tp) REVERT: F 133 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7906 (mp0) REVERT: H 25 LEU cc_start: 0.5775 (OUTLIER) cc_final: 0.5384 (tp) REVERT: H 57 GLN cc_start: 0.8444 (tp40) cc_final: 0.8160 (tp-100) REVERT: H 59 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8014 (mm) REVERT: H 136 MET cc_start: 0.7270 (mmp) cc_final: 0.7026 (mmm) outliers start: 50 outliers final: 21 residues processed: 214 average time/residue: 0.2299 time to fit residues: 65.6141 Evaluate side-chains 177 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 133 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 101 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 25 LEU 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 F residue 25 LEU Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 100 LEU 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 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 116 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 78 optimal weight: 0.2980 chunk 66 optimal weight: 0.4980 chunk 98 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4453 r_free = 0.4453 target = 0.189738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.168160 restraints weight = 12027.380| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 3.04 r_work: 0.4086 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.7396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9000 Z= 0.119 Angle : 0.582 7.554 12216 Z= 0.295 Chirality : 0.040 0.167 1352 Planarity : 0.006 0.063 1584 Dihedral : 4.021 13.499 1264 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 5.00 % Allowed : 15.94 % Favored : 79.06 % 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: 1.27 (0.26), residues: 1128 helix: 1.66 (0.25), residues: 472 sheet: 0.01 (0.48), residues: 136 loop : 0.45 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 4 HIS 0.002 0.000 HIS E 14 PHE 0.011 0.001 PHE D 73 TYR 0.015 0.002 TYR G 138 ARG 0.008 0.001 ARG G 129 Details of bonding type rmsd hydrogen bonds : bond 0.02787 ( 368) hydrogen bonds : angle 4.01909 ( 1047) covalent geometry : bond 0.00293 ( 9000) covalent geometry : angle 0.58170 (12216) *********************** 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 234 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 186 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 LEU cc_start: 0.5972 (OUTLIER) cc_final: 0.5416 (tp) REVERT: B 76 ASP cc_start: 0.8830 (t0) cc_final: 0.8534 (t0) REVERT: B 136 MET cc_start: 0.6935 (mmp) cc_final: 0.6649 (mmm) REVERT: A 76 ASP cc_start: 0.8807 (t0) cc_final: 0.8590 (t0) REVERT: C 25 LEU cc_start: 0.5815 (OUTLIER) cc_final: 0.5320 (tp) REVERT: C 76 ASP cc_start: 0.8797 (t0) cc_final: 0.8587 (t0) REVERT: C 136 MET cc_start: 0.7255 (mmp) cc_final: 0.6970 (mmm) REVERT: D 3 ARG cc_start: 0.4413 (tmm160) cc_final: 0.0634 (mmm160) REVERT: D 76 ASP cc_start: 0.8877 (t0) cc_final: 0.8502 (t0) REVERT: D 133 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7795 (mp0) REVERT: E 25 LEU cc_start: 0.5956 (OUTLIER) cc_final: 0.5525 (tp) REVERT: E 57 GLN cc_start: 0.8394 (tp40) cc_final: 0.8135 (tp-100) REVERT: F 18 ASP cc_start: 0.5763 (m-30) cc_final: 0.5127 (p0) REVERT: F 25 LEU cc_start: 0.6034 (OUTLIER) cc_final: 0.5826 (tp) REVERT: G 130 GLN cc_start: 0.5675 (tp40) cc_final: 0.5278 (mm-40) REVERT: G 133 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8117 (mp0) REVERT: H 25 LEU cc_start: 0.5627 (OUTLIER) cc_final: 0.5366 (tp) REVERT: H 57 GLN cc_start: 0.8525 (tp40) cc_final: 0.8232 (tp-100) REVERT: H 59 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7932 (mm) outliers start: 48 outliers final: 25 residues processed: 219 average time/residue: 0.2314 time to fit residues: 67.6328 Evaluate side-chains 188 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 19 LEU 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 100 LEU Chi-restraints excluded: chain C residue 101 LEU 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 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 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 25 LEU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain H residue 23 GLN 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 116 MET Chi-restraints excluded: chain H residue 131 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 91 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 82 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 108 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** G 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.188336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.166353 restraints weight = 12256.305| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 3.09 r_work: 0.4049 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.7887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9000 Z= 0.123 Angle : 0.597 7.341 12216 Z= 0.303 Chirality : 0.040 0.136 1352 Planarity : 0.006 0.085 1584 Dihedral : 3.992 14.573 1264 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.27 % Allowed : 18.23 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.26), residues: 1128 helix: 1.73 (0.25), residues: 472 sheet: -0.07 (0.48), residues: 136 loop : 0.44 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 4 HIS 0.001 0.000 HIS B 63 PHE 0.012 0.001 PHE A 73 TYR 0.015 0.002 TYR G 138 ARG 0.008 0.001 ARG G 137 Details of bonding type rmsd hydrogen bonds : bond 0.02814 ( 368) hydrogen bonds : angle 4.01291 ( 1047) covalent geometry : bond 0.00305 ( 9000) covalent geometry : angle 0.59733 (12216) *********************** 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 223 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 182 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 LEU cc_start: 0.6026 (OUTLIER) cc_final: 0.5550 (tp) REVERT: B 76 ASP cc_start: 0.8842 (t0) cc_final: 0.8451 (t0) REVERT: B 133 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7826 (mp0) REVERT: A 57 GLN cc_start: 0.8249 (tm-30) cc_final: 0.8033 (tp-100) REVERT: C 25 LEU cc_start: 0.5768 (OUTLIER) cc_final: 0.5335 (tp) REVERT: C 76 ASP cc_start: 0.8913 (t0) cc_final: 0.8709 (t0) REVERT: C 83 MET cc_start: 0.8879 (ptm) cc_final: 0.8615 (ttp) REVERT: D 3 ARG cc_start: 0.4644 (tmm160) cc_final: 0.0870 (mmm160) REVERT: D 57 GLN cc_start: 0.8440 (tp40) cc_final: 0.8163 (tp-100) REVERT: D 76 ASP cc_start: 0.8870 (t0) cc_final: 0.8648 (t0) REVERT: D 133 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7798 (mp0) REVERT: E 25 LEU cc_start: 0.5920 (OUTLIER) cc_final: 0.5571 (tp) REVERT: E 57 GLN cc_start: 0.8400 (tp40) cc_final: 0.8151 (tp-100) REVERT: F 18 ASP cc_start: 0.5770 (m-30) cc_final: 0.5160 (p0) REVERT: F 25 LEU cc_start: 0.6226 (OUTLIER) cc_final: 0.5847 (tp) REVERT: F 112 GLU cc_start: 0.7883 (mp0) cc_final: 0.7586 (mp0) REVERT: G 137 ARG cc_start: 0.7859 (mtm-85) cc_final: 0.7651 (mtm180) REVERT: H 57 GLN cc_start: 0.8560 (tp40) cc_final: 0.8283 (tp-100) REVERT: H 59 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7998 (mm) outliers start: 41 outliers final: 24 residues processed: 211 average time/residue: 0.2448 time to fit residues: 68.2293 Evaluate side-chains 193 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 133 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain C residue 19 LEU 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 100 LEU Chi-restraints excluded: chain C residue 101 LEU 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 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 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 25 LEU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 96 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 47 optimal weight: 4.9990 chunk 23 optimal weight: 0.0570 chunk 55 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 96 optimal weight: 0.0980 chunk 84 optimal weight: 3.9990 chunk 102 optimal weight: 0.1980 overall best weight: 0.3898 ------------------------------------------------------------------------------- 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 = 0.4447 r_free = 0.4447 target = 0.189000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.167459 restraints weight = 12452.785| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 3.10 r_work: 0.4071 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.8123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9000 Z= 0.114 Angle : 0.588 7.016 12216 Z= 0.297 Chirality : 0.039 0.115 1352 Planarity : 0.005 0.050 1584 Dihedral : 3.897 16.463 1264 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.96 % Allowed : 19.58 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.26), residues: 1128 helix: 1.75 (0.25), residues: 480 sheet: -0.08 (0.48), residues: 136 loop : 0.53 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 4 HIS 0.002 0.001 HIS H 63 PHE 0.011 0.001 PHE D 73 TYR 0.014 0.001 TYR G 138 ARG 0.005 0.000 ARG E 37 Details of bonding type rmsd hydrogen bonds : bond 0.02568 ( 368) hydrogen bonds : angle 3.94647 ( 1047) covalent geometry : bond 0.00285 ( 9000) covalent geometry : angle 0.58828 (12216) *********************** 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 223 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 GLN cc_start: 0.8371 (tp40) cc_final: 0.8148 (tp-100) REVERT: B 76 ASP cc_start: 0.8775 (t0) cc_final: 0.8532 (t0) REVERT: B 133 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: A 6 LYS cc_start: 0.6173 (tppt) cc_final: 0.5539 (tppt) REVERT: A 18 ASP cc_start: 0.5428 (p0) cc_final: 0.5222 (p0) REVERT: C 25 LEU cc_start: 0.5742 (OUTLIER) cc_final: 0.5370 (tp) REVERT: D 3 ARG cc_start: 0.4866 (tmm160) cc_final: 0.1228 (mmm160) REVERT: D 57 GLN cc_start: 0.8428 (tp40) cc_final: 0.8121 (tp-100) REVERT: D 76 ASP cc_start: 0.8804 (t0) cc_final: 0.8602 (t0) REVERT: D 133 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: E 25 LEU cc_start: 0.5824 (OUTLIER) cc_final: 0.5549 (tp) REVERT: E 57 GLN cc_start: 0.8377 (tp40) cc_final: 0.8145 (tp-100) REVERT: E 130 GLN cc_start: 0.5514 (tp40) cc_final: 0.5298 (mm-40) REVERT: E 133 GLU cc_start: 0.8582 (tt0) cc_final: 0.8073 (mp0) REVERT: F 18 ASP cc_start: 0.5799 (m-30) cc_final: 0.5151 (p0) REVERT: F 19 LEU cc_start: 0.7231 (tp) cc_final: 0.6939 (tt) REVERT: F 25 LEU cc_start: 0.6128 (OUTLIER) cc_final: 0.5771 (tp) REVERT: G 25 LEU cc_start: 0.5947 (OUTLIER) cc_final: 0.5594 (tp) REVERT: G 136 MET cc_start: 0.6871 (mmp) cc_final: 0.6652 (mmm) REVERT: H 36 LEU cc_start: 0.1984 (OUTLIER) cc_final: 0.1745 (mp) REVERT: H 57 GLN cc_start: 0.8549 (tp40) cc_final: 0.8266 (tp-100) REVERT: H 59 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7989 (mm) outliers start: 38 outliers final: 22 residues processed: 213 average time/residue: 0.2649 time to fit residues: 74.6517 Evaluate side-chains 193 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 101 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 100 LEU 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 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 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 25 LEU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 100 LEU 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 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 81 optimal weight: 0.0870 chunk 78 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 57 optimal weight: 0.2980 overall best weight: 0.8764 ------------------------------------------------------------------------------- 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 = 0.4446 r_free = 0.4446 target = 0.189576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.172572 restraints weight = 12297.155| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 2.23 r_work: 0.4103 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.8582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9000 Z= 0.141 Angle : 0.637 6.904 12216 Z= 0.324 Chirality : 0.041 0.147 1352 Planarity : 0.006 0.063 1584 Dihedral : 4.023 16.295 1264 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.17 % Allowed : 19.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.26), residues: 1128 helix: 1.65 (0.25), residues: 480 sheet: -0.11 (0.49), residues: 136 loop : 0.45 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 4 HIS 0.001 0.000 HIS G 14 PHE 0.012 0.001 PHE H 73 TYR 0.018 0.002 TYR G 138 ARG 0.008 0.001 ARG H 129 Details of bonding type rmsd hydrogen bonds : bond 0.03041 ( 368) hydrogen bonds : angle 3.99724 ( 1047) covalent geometry : bond 0.00349 ( 9000) covalent geometry : angle 0.63731 (12216) *********************** 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 210 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 GLN cc_start: 0.8484 (tp40) cc_final: 0.8280 (tp-100) REVERT: A 18 ASP cc_start: 0.5755 (p0) cc_final: 0.5313 (p0) REVERT: C 25 LEU cc_start: 0.5702 (OUTLIER) cc_final: 0.5337 (tp) REVERT: D 3 ARG cc_start: 0.4825 (tmm160) cc_final: 0.1243 (mmm160) REVERT: D 116 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8318 (ptp) REVERT: E 25 LEU cc_start: 0.5913 (OUTLIER) cc_final: 0.5643 (tp) REVERT: F 18 ASP cc_start: 0.5602 (m-30) cc_final: 0.5352 (p0) REVERT: F 19 LEU cc_start: 0.7091 (tp) cc_final: 0.6868 (tt) REVERT: F 25 LEU cc_start: 0.6166 (OUTLIER) cc_final: 0.5840 (tp) REVERT: F 112 GLU cc_start: 0.7524 (mp0) cc_final: 0.7210 (mp0) REVERT: F 136 MET cc_start: 0.6795 (mmm) cc_final: 0.6518 (mmp) REVERT: G 18 ASP cc_start: 0.6420 (p0) cc_final: 0.6203 (p0) REVERT: H 36 LEU cc_start: 0.2369 (OUTLIER) cc_final: 0.2030 (mp) REVERT: H 59 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8299 (mm) REVERT: H 83 MET cc_start: 0.8784 (ttp) cc_final: 0.8576 (ttp) REVERT: H 137 ARG cc_start: 0.7708 (ptp90) cc_final: 0.7458 (ptp90) outliers start: 40 outliers final: 24 residues processed: 198 average time/residue: 0.2436 time to fit residues: 63.8298 Evaluate side-chains 187 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain C residue 19 LEU 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 19 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 116 MET 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 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 25 LEU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 96 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.183321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.166272 restraints weight = 12418.214| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 2.24 r_work: 0.4043 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.9288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9000 Z= 0.192 Angle : 0.721 8.679 12216 Z= 0.371 Chirality : 0.045 0.210 1352 Planarity : 0.006 0.052 1584 Dihedral : 4.389 16.095 1264 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.96 % Allowed : 19.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.26), residues: 1128 helix: 1.45 (0.25), residues: 472 sheet: -0.39 (0.48), residues: 136 loop : 0.22 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 4 HIS 0.002 0.001 HIS G 14 PHE 0.015 0.002 PHE H 73 TYR 0.021 0.002 TYR F 109 ARG 0.009 0.001 ARG D 137 Details of bonding type rmsd hydrogen bonds : bond 0.03915 ( 368) hydrogen bonds : angle 4.22803 ( 1047) covalent geometry : bond 0.00475 ( 9000) covalent geometry : angle 0.72145 (12216) *********************** 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 237 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.6031 (tppt) cc_final: 0.5453 (tppt) REVERT: A 18 ASP cc_start: 0.5687 (p0) cc_final: 0.5224 (p0) REVERT: C 25 LEU cc_start: 0.5849 (OUTLIER) cc_final: 0.5346 (tp) REVERT: D 3 ARG cc_start: 0.5198 (tmm160) cc_final: 0.0996 (mmm160) REVERT: D 101 LEU cc_start: 0.6772 (mm) cc_final: 0.6397 (tt) REVERT: E 25 LEU cc_start: 0.6037 (OUTLIER) cc_final: 0.5565 (tp) REVERT: F 18 ASP cc_start: 0.5695 (m-30) cc_final: 0.5429 (p0) REVERT: F 19 LEU cc_start: 0.7153 (tp) cc_final: 0.6894 (tt) REVERT: G 136 MET cc_start: 0.6444 (mmp) cc_final: 0.6154 (mmm) REVERT: H 137 ARG cc_start: 0.7685 (ptp90) cc_final: 0.7467 (mtm-85) outliers start: 38 outliers final: 22 residues processed: 228 average time/residue: 0.2800 time to fit residues: 81.7773 Evaluate side-chains 203 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 179 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 101 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 D residue 19 LEU Chi-restraints excluded: chain D residue 66 VAL 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 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 96 CYS Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain H residue 36 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 35 optimal weight: 2.9990 chunk 77 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 55 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.4378 r_free = 0.4378 target = 0.183218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.165741 restraints weight = 12450.386| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 2.29 r_work: 0.4054 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.9649 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= 0.151 Angle : 0.698 8.010 12216 Z= 0.351 Chirality : 0.043 0.264 1352 Planarity : 0.005 0.053 1584 Dihedral : 4.226 18.573 1264 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.92 % Allowed : 21.25 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.26), residues: 1128 helix: 1.59 (0.26), residues: 472 sheet: -0.50 (0.48), residues: 136 loop : 0.21 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 4 HIS 0.001 0.000 HIS A 14 PHE 0.011 0.001 PHE H 73 TYR 0.020 0.002 TYR G 138 ARG 0.006 0.001 ARG E 37 Details of bonding type rmsd hydrogen bonds : bond 0.03317 ( 368) hydrogen bonds : angle 4.20195 ( 1047) covalent geometry : bond 0.00379 ( 9000) covalent geometry : angle 0.69809 (12216) ********************** 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 213 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: A 6 LYS cc_start: 0.6142 (tppt) cc_final: 0.5396 (tppt) REVERT: A 18 ASP cc_start: 0.5637 (p0) cc_final: 0.5173 (p0) REVERT: C 25 LEU cc_start: 0.5793 (OUTLIER) cc_final: 0.5383 (tp) REVERT: C 57 GLN cc_start: 0.8377 (tp40) cc_final: 0.8174 (tp-100) REVERT: D 3 ARG cc_start: 0.4993 (tmm160) cc_final: 0.0874 (ptm160) REVERT: D 101 LEU cc_start: 0.6695 (mm) cc_final: 0.6326 (tt) REVERT: D 136 MET cc_start: 0.6526 (mmp) cc_final: 0.6277 (mmm) REVERT: E 25 LEU cc_start: 0.5889 (OUTLIER) cc_final: 0.5649 (tp) REVERT: H 137 ARG cc_start: 0.7644 (ptp90) cc_final: 0.7399 (ptp-170) outliers start: 28 outliers final: 23 residues processed: 206 average time/residue: 0.2490 time to fit residues: 67.1807 Evaluate side-chains 196 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain C residue 19 LEU 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 D residue 19 LEU Chi-restraints excluded: chain D residue 66 VAL 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 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 96 CYS Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain H residue 36 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 78 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.177407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.159986 restraints weight = 12501.968| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 2.28 r_work: 0.3981 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 1.0132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9000 Z= 0.260 Angle : 0.812 7.768 12216 Z= 0.418 Chirality : 0.050 0.277 1352 Planarity : 0.007 0.055 1584 Dihedral : 4.838 17.411 1264 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.92 % Allowed : 21.35 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1128 helix: 0.85 (0.25), residues: 464 sheet: -0.70 (0.49), residues: 136 loop : -0.18 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP C 4 HIS 0.003 0.001 HIS B 63 PHE 0.019 0.002 PHE H 73 TYR 0.024 0.003 TYR G 138 ARG 0.010 0.001 ARG C 37 Details of bonding type rmsd hydrogen bonds : bond 0.04783 ( 368) hydrogen bonds : angle 4.62531 ( 1047) covalent geometry : bond 0.00642 ( 9000) covalent geometry : angle 0.81189 (12216) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3786.94 seconds wall clock time: 66 minutes 9.49 seconds (3969.49 seconds total)