Starting phenix.real_space_refine on Sun Apr 5 14:00:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nci_12267/04_2026/7nci_12267.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nci_12267/04_2026/7nci_12267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nci_12267/04_2026/7nci_12267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nci_12267/04_2026/7nci_12267.map" model { file = "/net/cci-nas-00/data/ceres_data/7nci_12267/04_2026/7nci_12267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nci_12267/04_2026/7nci_12267.cif" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians C 3408 2.51 5 N 972 2.21 5 O 1116 1.98 5 H 5796 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11292 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "B" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "C" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "D" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "E" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "F" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "G" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "I" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "J" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "K" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "L" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Time building chain proxies: 1.76, per 1000 atoms: 0.16 Number of scatterers: 11292 At special positions: 0 Unit cell: (119.9, 95.7, 56.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 1116 8.00 N 972 7.00 C 3408 6.00 H 5796 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 323.1 milliseconds 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1368 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 21 removed outlier: 7.195A pdb=" N ALA A 18 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 9.452A pdb=" N LYS B 21 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N GLU A 20 " --> pdb=" O LYS B 21 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA C 19 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS C 21 " --> pdb=" O GLU B 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 41 removed outlier: 5.672A pdb=" N TYR A 39 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N TYR B 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N TYR C 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY D 41 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N TYR E 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 55 removed outlier: 4.650A pdb=" N VAL A 49 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N GLY B 51 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N GLY A 51 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ALA B 53 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ALA A 53 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL B 55 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A 55 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N VAL B 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 10.372A pdb=" N VAL C 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY B 51 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N THR C 54 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA B 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY D 51 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL C 52 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA D 53 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N THR C 54 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL D 55 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 9.025A pdb=" N HIS D 50 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ALA E 53 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 9.108A pdb=" N VAL D 52 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 10.794A pdb=" N VAL E 55 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N THR D 54 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N HIS E 50 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ALA F 53 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N VAL E 52 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 10.619A pdb=" N VAL F 55 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N THR E 54 " --> pdb=" O VAL F 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 63 through 64 removed outlier: 7.057A pdb=" N VAL A 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL B 63 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N VAL C 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL D 66 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL E 63 " --> pdb=" O THR F 64 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 85 through 88 removed outlier: 6.399A pdb=" N GLY B 86 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY C 86 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N ALA D 89 " --> pdb=" O GLY C 86 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE C 88 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY D 86 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N ALA E 89 " --> pdb=" O GLY D 86 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE D 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLY E 86 " --> pdb=" O SER F 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 18 through 21 removed outlier: 3.790A pdb=" N ALA E 19 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS E 21 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA F 17 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS F 21 " --> pdb=" O GLU E 20 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 18 through 21 removed outlier: 7.012A pdb=" N ALA G 18 " --> pdb=" O ALA H 19 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N LYS H 21 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N GLU G 20 " --> pdb=" O LYS H 21 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA I 19 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS I 21 " --> pdb=" O GLU H 20 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA J 19 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU I 20 " --> pdb=" O ALA J 19 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS J 21 " --> pdb=" O GLU I 20 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA K 19 " --> pdb=" O ALA J 18 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS K 21 " --> pdb=" O GLU J 20 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA L 19 " --> pdb=" O ALA K 18 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU K 20 " --> pdb=" O ALA L 19 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS L 21 " --> pdb=" O GLU K 20 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 39 through 41 removed outlier: 5.540A pdb=" N TYR G 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N TYR H 39 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N TYR I 39 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N TYR J 39 " --> pdb=" O VAL K 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 49 through 55 removed outlier: 9.310A pdb=" N VAL G 49 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 10.589A pdb=" N VAL H 52 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLY G 51 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N THR H 54 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA G 53 " --> pdb=" O THR H 54 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N HIS H 50 " --> pdb=" O GLY I 51 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ALA I 53 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N VAL H 52 " --> pdb=" O ALA I 53 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N VAL I 55 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N THR H 54 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N HIS I 50 " --> pdb=" O GLY J 51 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ALA J 53 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 9.026A pdb=" N VAL I 52 " --> pdb=" O ALA J 53 " (cutoff:3.500A) removed outlier: 10.661A pdb=" N VAL J 55 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 8.932A pdb=" N THR I 54 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N HIS J 50 " --> pdb=" O GLY K 51 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ALA K 53 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 9.085A pdb=" N VAL J 52 " --> pdb=" O ALA K 53 " (cutoff:3.500A) removed outlier: 10.710A pdb=" N VAL K 55 " --> pdb=" O VAL J 52 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N THR J 54 " --> pdb=" O VAL K 55 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N HIS K 50 " --> pdb=" O GLY L 51 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ALA L 53 " --> pdb=" O HIS K 50 " (cutoff:3.500A) removed outlier: 9.215A pdb=" N VAL K 52 " --> pdb=" O ALA L 53 " (cutoff:3.500A) removed outlier: 10.709A pdb=" N VAL L 55 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N THR K 54 " --> pdb=" O VAL L 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 63 through 66 removed outlier: 3.579A pdb=" N VAL H 66 " --> pdb=" O ASN G 65 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N VAL I 63 " --> pdb=" O THR J 64 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL J 63 " --> pdb=" O THR K 64 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL K 63 " --> pdb=" O THR L 64 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 86 through 90 removed outlier: 6.516A pdb=" N GLY G 86 " --> pdb=" O SER H 87 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N ALA H 89 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE G 88 " --> pdb=" O ALA H 89 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLY H 86 " --> pdb=" O SER I 87 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLY I 86 " --> pdb=" O SER J 87 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY J 86 " --> pdb=" O SER K 87 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N ALA K 89 " --> pdb=" O GLY J 86 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE J 88 " --> pdb=" O ALA K 89 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLY K 86 " --> pdb=" O SER L 87 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N ALA L 89 " --> pdb=" O GLY K 86 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE K 88 " --> pdb=" O ALA L 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 18 hydrogen bonds defined for protein. 51 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: 2.06 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 0.97: 1817 0.97 - 1.12: 3979 1.12 - 1.28: 984 1.28 - 1.43: 1075 1.43 - 1.59: 3437 Bond restraints: 11292 Sorted by residual: bond pdb=" N VAL G 40 " pdb=" CA VAL G 40 " ideal model delta sigma weight residual 1.460 1.501 -0.041 1.44e-02 4.82e+03 8.11e+00 bond pdb=" N VAL J 40 " pdb=" CA VAL J 40 " ideal model delta sigma weight residual 1.461 1.501 -0.040 1.44e-02 4.82e+03 7.85e+00 bond pdb=" CA ILE A 88 " pdb=" CB ILE A 88 " ideal model delta sigma weight residual 1.548 1.587 -0.040 1.46e-02 4.69e+03 7.35e+00 bond pdb=" N VAL B 40 " pdb=" CA VAL B 40 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.44e-02 4.82e+03 5.53e+00 bond pdb=" N VAL A 40 " pdb=" CA VAL A 40 " ideal model delta sigma weight residual 1.460 1.490 -0.030 1.35e-02 5.49e+03 4.93e+00 ... (remaining 11287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.36: 20524 7.36 - 14.73: 2 14.73 - 22.09: 0 22.09 - 29.46: 2 29.46 - 36.82: 4 Bond angle restraints: 20532 Sorted by residual: angle pdb=" N THR C 44 " pdb=" CA THR C 44 " pdb=" HA THR C 44 " ideal model delta sigma weight residual 110.00 73.18 36.82 3.00e+00 1.11e-01 1.51e+02 angle pdb=" C THR I 44 " pdb=" CA THR I 44 " pdb=" HA THR I 44 " ideal model delta sigma weight residual 109.00 73.72 35.28 3.00e+00 1.11e-01 1.38e+02 angle pdb=" C THR C 44 " pdb=" CA THR C 44 " pdb=" HA THR C 44 " ideal model delta sigma weight residual 109.00 74.54 34.46 3.00e+00 1.11e-01 1.32e+02 angle pdb=" N THR I 44 " pdb=" CA THR I 44 " pdb=" HA THR I 44 " ideal model delta sigma weight residual 110.00 75.68 34.32 3.00e+00 1.11e-01 1.31e+02 angle pdb=" CB THR I 44 " pdb=" CA THR I 44 " pdb=" HA THR I 44 " ideal model delta sigma weight residual 109.00 80.08 28.92 3.00e+00 1.11e-01 9.29e+01 ... (remaining 20527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 4359 17.86 - 35.72: 362 35.72 - 53.58: 141 53.58 - 71.44: 272 71.44 - 89.30: 26 Dihedral angle restraints: 5160 sinusoidal: 2904 harmonic: 2256 Sorted by residual: dihedral pdb=" C THR I 44 " pdb=" N THR I 44 " pdb=" CA THR I 44 " pdb=" CB THR I 44 " ideal model delta harmonic sigma weight residual -122.00 -136.89 14.89 0 2.50e+00 1.60e-01 3.55e+01 dihedral pdb=" CA VAL E 74 " pdb=" C VAL E 74 " pdb=" N THR E 75 " pdb=" CA THR E 75 " ideal model delta harmonic sigma weight residual 180.00 150.91 29.09 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA SER A 87 " pdb=" C SER A 87 " pdb=" N ILE A 88 " pdb=" CA ILE A 88 " ideal model delta harmonic sigma weight residual 180.00 151.03 28.97 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 5157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 740 0.107 - 0.213: 208 0.213 - 0.320: 34 0.320 - 0.427: 0 0.427 - 0.533: 2 Chirality restraints: 984 Sorted by residual: chirality pdb=" CA THR I 44 " pdb=" N THR I 44 " pdb=" C THR I 44 " pdb=" CB THR I 44 " both_signs ideal model delta sigma weight residual False 2.53 1.99 0.53 2.00e-01 2.50e+01 7.11e+00 chirality pdb=" CA THR C 44 " pdb=" N THR C 44 " pdb=" C THR C 44 " pdb=" CB THR C 44 " both_signs ideal model delta sigma weight residual False 2.53 2.05 0.48 2.00e-01 2.50e+01 5.77e+00 chirality pdb=" CB VAL J 40 " pdb=" CA VAL J 40 " pdb=" CG1 VAL J 40 " pdb=" CG2 VAL J 40 " both_signs ideal model delta sigma weight residual False -2.63 -2.91 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 981 not shown) Planarity restraints: 1716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 39 " 0.077 2.00e-02 2.50e+03 3.32e-02 3.32e+01 pdb=" CG TYR L 39 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR L 39 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR L 39 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR L 39 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR L 39 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR L 39 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR L 39 " 0.021 2.00e-02 2.50e+03 pdb=" HD1 TYR L 39 " -0.038 2.00e-02 2.50e+03 pdb=" HD2 TYR L 39 " -0.021 2.00e-02 2.50e+03 pdb=" HE1 TYR L 39 " 0.025 2.00e-02 2.50e+03 pdb=" HE2 TYR L 39 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 39 " -0.025 2.00e-02 2.50e+03 3.16e-02 2.99e+01 pdb=" CG TYR B 39 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 TYR B 39 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B 39 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR B 39 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR B 39 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYR B 39 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR B 39 " -0.017 2.00e-02 2.50e+03 pdb=" HD1 TYR B 39 " -0.030 2.00e-02 2.50e+03 pdb=" HD2 TYR B 39 " -0.040 2.00e-02 2.50e+03 pdb=" HE1 TYR B 39 " -0.009 2.00e-02 2.50e+03 pdb=" HE2 TYR B 39 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 39 " 0.004 2.00e-02 2.50e+03 2.79e-02 2.33e+01 pdb=" CG TYR K 39 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 TYR K 39 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR K 39 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR K 39 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR K 39 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR K 39 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR K 39 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 TYR K 39 " 0.027 2.00e-02 2.50e+03 pdb=" HD2 TYR K 39 " 0.047 2.00e-02 2.50e+03 pdb=" HE1 TYR K 39 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR K 39 " 0.009 2.00e-02 2.50e+03 ... (remaining 1713 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.22: 665 2.22 - 2.79: 22320 2.79 - 3.36: 26919 3.36 - 3.93: 34152 3.93 - 4.50: 52195 Nonbonded interactions: 136251 Sorted by model distance: nonbonded pdb=" H THR C 44 " pdb=" HA THR C 44 " model vdw 1.651 1.816 nonbonded pdb=" HG1 THR C 44 " pdb=" O THR D 44 " model vdw 1.680 2.450 nonbonded pdb=" HG1 THR I 44 " pdb=" O THR J 44 " model vdw 1.691 2.450 nonbonded pdb=" H THR I 44 " pdb=" HA THR I 44 " model vdw 1.692 1.816 nonbonded pdb=" HG1 THR H 44 " pdb=" O THR I 44 " model vdw 1.695 2.450 ... (remaining 136246 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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 group one per residue 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: 1.010 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: 0.040 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.500 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6186 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 : 0.012 0.068 5496 Z= 0.645 Angle : 1.574 9.424 7416 Z= 0.948 Chirality : 0.101 0.533 984 Planarity : 0.005 0.034 924 Dihedral : 15.566 89.302 1848 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 0.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.74 (0.16), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.13), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.061 0.017 TYR B 39 HIS 0.026 0.011 HIS L 50 Details of bonding type rmsd covalent geometry : bond 0.01156 ( 5496) covalent geometry : angle 1.57430 ( 7416) hydrogen bonds : bond 0.42480 ( 18) hydrogen bonds : angle 13.75845 ( 51) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.1989 time to fit residues: 52.2272 Evaluate side-chains 112 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.0050 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5379 r_free = 0.5379 target = 0.258485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5116 r_free = 0.5116 target = 0.194196 restraints weight = 25508.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.5223 r_free = 0.5223 target = 0.205019 restraints weight = 12413.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.5295 r_free = 0.5295 target = 0.212865 restraints weight = 7317.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.5343 r_free = 0.5343 target = 0.218658 restraints weight = 4782.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.5373 r_free = 0.5373 target = 0.222369 restraints weight = 3284.217| |-----------------------------------------------------------------------------| r_work (final): 0.5285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5645 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5496 Z= 0.155 Angle : 0.659 5.074 7416 Z= 0.383 Chirality : 0.054 0.364 984 Planarity : 0.002 0.010 924 Dihedral : 8.080 22.983 804 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 2.41 % Allowed : 18.33 % Favored : 79.26 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.02 (0.16), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.12), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.003 TYR L 39 HIS 0.005 0.002 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 5496) covalent geometry : angle 0.65878 ( 7416) hydrogen bonds : bond 0.09428 ( 18) hydrogen bonds : angle 12.59802 ( 51) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.6295 (mttt) cc_final: 0.6082 (mmtp) REVERT: C 45 LYS cc_start: 0.7261 (mttt) cc_final: 0.6874 (ttpt) REVERT: H 20 GLU cc_start: 0.7851 (pp20) cc_final: 0.7650 (pp20) outliers start: 13 outliers final: 10 residues processed: 137 average time/residue: 0.1601 time to fit residues: 28.8873 Evaluate side-chains 126 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain K residue 39 TYR Chi-restraints excluded: chain K residue 65 ASN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 65 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 65 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 0.0980 chunk 37 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 HIS ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 HIS ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5350 r_free = 0.5350 target = 0.250496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.5096 r_free = 0.5096 target = 0.189511 restraints weight = 25748.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5189 r_free = 0.5189 target = 0.199838 restraints weight = 12551.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.5259 r_free = 0.5259 target = 0.207382 restraints weight = 7443.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.5307 r_free = 0.5307 target = 0.212800 restraints weight = 4896.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.5339 r_free = 0.5339 target = 0.216516 restraints weight = 3415.472| |-----------------------------------------------------------------------------| r_work (final): 0.5218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5809 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5496 Z= 0.161 Angle : 0.601 5.199 7416 Z= 0.347 Chirality : 0.054 0.389 984 Planarity : 0.002 0.007 924 Dihedral : 7.092 20.322 804 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 5.37 % Allowed : 22.04 % Favored : 72.59 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.71 (0.21), residues: 768 helix: None (None), residues: 0 sheet: -0.96 (0.45), residues: 120 loop : -3.09 (0.16), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.002 TYR L 39 HIS 0.005 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 5496) covalent geometry : angle 0.60120 ( 7416) hydrogen bonds : bond 0.08733 ( 18) hydrogen bonds : angle 11.50121 ( 51) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.6343 (mttt) cc_final: 0.6130 (mmtp) REVERT: C 45 LYS cc_start: 0.7241 (mmtt) cc_final: 0.6803 (ttpt) REVERT: C 46 GLU cc_start: 0.7790 (pp20) cc_final: 0.7525 (pp20) outliers start: 29 outliers final: 25 residues processed: 132 average time/residue: 0.1750 time to fit residues: 29.8740 Evaluate side-chains 137 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 65 ASN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 65 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN I 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5347 r_free = 0.5347 target = 0.217273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.5053 r_free = 0.5053 target = 0.184583 restraints weight = 23707.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.5139 r_free = 0.5139 target = 0.193689 restraints weight = 11297.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.5195 r_free = 0.5195 target = 0.200261 restraints weight = 6537.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.5231 r_free = 0.5231 target = 0.204798 restraints weight = 4187.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.5261 r_free = 0.5261 target = 0.208238 restraints weight = 2867.483| |-----------------------------------------------------------------------------| r_work (final): 0.5245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6234 moved from start: 0.5530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5496 Z= 0.132 Angle : 0.527 5.019 7416 Z= 0.306 Chirality : 0.053 0.377 984 Planarity : 0.001 0.007 924 Dihedral : 6.514 18.137 804 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 5.00 % Allowed : 22.96 % Favored : 72.04 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.59 (0.22), residues: 768 helix: None (None), residues: 0 sheet: -0.91 (0.46), residues: 120 loop : -2.99 (0.17), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR L 39 HIS 0.003 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 5496) covalent geometry : angle 0.52685 ( 7416) hydrogen bonds : bond 0.07217 ( 18) hydrogen bonds : angle 10.80744 ( 51) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 LYS cc_start: 0.7169 (mmtt) cc_final: 0.6848 (ttpt) REVERT: C 46 GLU cc_start: 0.7996 (pp20) cc_final: 0.7609 (pp20) REVERT: D 80 LYS cc_start: 0.8505 (ttpt) cc_final: 0.7991 (mttp) outliers start: 27 outliers final: 23 residues processed: 125 average time/residue: 0.1634 time to fit residues: 26.8907 Evaluate side-chains 136 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 65 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 43 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 4 optimal weight: 0.0970 chunk 6 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** 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 = 0.5268 r_free = 0.5268 target = 0.209793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4998 r_free = 0.4998 target = 0.179663 restraints weight = 22816.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5071 r_free = 0.5071 target = 0.187992 restraints weight = 10899.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.5128 r_free = 0.5128 target = 0.194113 restraints weight = 6289.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.5160 r_free = 0.5160 target = 0.198362 restraints weight = 3984.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.5188 r_free = 0.5188 target = 0.201466 restraints weight = 2686.154| |-----------------------------------------------------------------------------| r_work (final): 0.5200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 moved from start: 0.5919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5496 Z= 0.183 Angle : 0.560 5.162 7416 Z= 0.326 Chirality : 0.053 0.381 984 Planarity : 0.002 0.008 924 Dihedral : 6.710 19.651 804 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer: Outliers : 7.22 % Allowed : 22.41 % Favored : 70.37 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.19 (0.19), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.15), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.001 TYR L 39 HIS 0.005 0.002 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 5496) covalent geometry : angle 0.56050 ( 7416) hydrogen bonds : bond 0.07903 ( 18) hydrogen bonds : angle 10.61131 ( 51) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 112 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 LYS cc_start: 0.7087 (mmtt) cc_final: 0.6816 (ttpt) REVERT: C 46 GLU cc_start: 0.8116 (pp20) cc_final: 0.7455 (pp20) REVERT: D 80 LYS cc_start: 0.8582 (ttpt) cc_final: 0.8074 (mttp) outliers start: 39 outliers final: 33 residues processed: 127 average time/residue: 0.1433 time to fit residues: 24.6585 Evaluate side-chains 139 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 65 ASN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 65 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 12 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** 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 = 0.5265 r_free = 0.5265 target = 0.208278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4998 r_free = 0.4998 target = 0.178454 restraints weight = 22871.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5074 r_free = 0.5074 target = 0.186681 restraints weight = 10947.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.5127 r_free = 0.5127 target = 0.192722 restraints weight = 6302.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.5160 r_free = 0.5160 target = 0.196938 restraints weight = 3982.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.5184 r_free = 0.5184 target = 0.199870 restraints weight = 2667.032| |-----------------------------------------------------------------------------| r_work (final): 0.5194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6398 moved from start: 0.6300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5496 Z= 0.192 Angle : 0.566 5.292 7416 Z= 0.329 Chirality : 0.053 0.387 984 Planarity : 0.002 0.008 924 Dihedral : 6.859 21.068 804 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.98 % Favored : 88.02 % Rotamer: Outliers : 7.96 % Allowed : 22.78 % Favored : 69.26 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.28 (0.20), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.15), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR J 39 HIS 0.005 0.002 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 5496) covalent geometry : angle 0.56596 ( 7416) hydrogen bonds : bond 0.07348 ( 18) hydrogen bonds : angle 10.69520 ( 51) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 101 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 45 LYS cc_start: 0.7107 (mmtt) cc_final: 0.6822 (ttpt) REVERT: D 75 THR cc_start: 0.7914 (OUTLIER) cc_final: 0.7708 (t) REVERT: D 80 LYS cc_start: 0.8596 (ttpt) cc_final: 0.8085 (mttp) outliers start: 43 outliers final: 38 residues processed: 120 average time/residue: 0.1489 time to fit residues: 24.0023 Evaluate side-chains 140 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 101 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 65 ASN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 65 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** 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 = 0.5279 r_free = 0.5279 target = 0.208745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5015 r_free = 0.5015 target = 0.179524 restraints weight = 23113.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.5088 r_free = 0.5088 target = 0.187693 restraints weight = 11112.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.5139 r_free = 0.5139 target = 0.193551 restraints weight = 6395.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.5172 r_free = 0.5172 target = 0.197739 restraints weight = 4043.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.5195 r_free = 0.5195 target = 0.200539 restraints weight = 2703.443| |-----------------------------------------------------------------------------| r_work (final): 0.5214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 moved from start: 0.6543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5496 Z= 0.166 Angle : 0.535 5.003 7416 Z= 0.312 Chirality : 0.053 0.382 984 Planarity : 0.002 0.006 924 Dihedral : 6.548 20.353 804 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.11 % Favored : 87.89 % Rotamer: Outliers : 7.41 % Allowed : 24.26 % Favored : 68.33 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.33 (0.20), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.15), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.001 TYR J 39 HIS 0.004 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 5496) covalent geometry : angle 0.53463 ( 7416) hydrogen bonds : bond 0.06731 ( 18) hydrogen bonds : angle 10.24980 ( 51) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 LYS cc_start: 0.7136 (mmtt) cc_final: 0.6907 (ttpt) REVERT: D 80 LYS cc_start: 0.8606 (ttpt) cc_final: 0.8090 (mttp) outliers start: 40 outliers final: 36 residues processed: 129 average time/residue: 0.1720 time to fit residues: 29.2059 Evaluate side-chains 141 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 65 ASN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 50 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 = 0.5277 r_free = 0.5277 target = 0.207877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5003 r_free = 0.5003 target = 0.178237 restraints weight = 23206.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.5083 r_free = 0.5083 target = 0.186443 restraints weight = 11130.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.5134 r_free = 0.5134 target = 0.192397 restraints weight = 6394.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.5163 r_free = 0.5163 target = 0.196243 restraints weight = 4026.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.5189 r_free = 0.5189 target = 0.199256 restraints weight = 2777.477| |-----------------------------------------------------------------------------| r_work (final): 0.5207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.6818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5496 Z= 0.188 Angle : 0.552 5.154 7416 Z= 0.322 Chirality : 0.053 0.385 984 Planarity : 0.002 0.010 924 Dihedral : 6.693 21.279 804 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.67 % Favored : 86.33 % Rotamer: Outliers : 8.52 % Allowed : 23.52 % Favored : 67.96 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.39 (0.20), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.15), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.001 TYR J 39 HIS 0.004 0.001 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 5496) covalent geometry : angle 0.55242 ( 7416) hydrogen bonds : bond 0.06723 ( 18) hydrogen bonds : angle 10.34900 ( 51) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 101 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 LYS cc_start: 0.7165 (mmtt) cc_final: 0.6937 (ttpt) REVERT: C 70 VAL cc_start: 0.7431 (OUTLIER) cc_final: 0.6845 (t) REVERT: D 80 LYS cc_start: 0.8630 (ttpt) cc_final: 0.8113 (mttp) outliers start: 46 outliers final: 40 residues processed: 121 average time/residue: 0.1700 time to fit residues: 26.9436 Evaluate side-chains 142 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 101 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 65 ASN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 80 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 48 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 35 optimal weight: 0.0270 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 50 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 = 0.5355 r_free = 0.5355 target = 0.248661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.5113 r_free = 0.5113 target = 0.187834 restraints weight = 25372.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.5207 r_free = 0.5207 target = 0.197819 restraints weight = 12557.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.5269 r_free = 0.5269 target = 0.205032 restraints weight = 7459.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.5314 r_free = 0.5314 target = 0.210178 restraints weight = 4874.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.5344 r_free = 0.5344 target = 0.213777 restraints weight = 3388.871| |-----------------------------------------------------------------------------| r_work (final): 0.5223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 moved from start: 0.6941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5496 Z= 0.116 Angle : 0.479 4.817 7416 Z= 0.279 Chirality : 0.053 0.378 984 Planarity : 0.001 0.008 924 Dihedral : 5.957 18.951 804 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer: Outliers : 5.00 % Allowed : 26.30 % Favored : 68.70 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.21 (0.20), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.16), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR J 39 HIS 0.002 0.001 HIS L 50 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 5496) covalent geometry : angle 0.47928 ( 7416) hydrogen bonds : bond 0.05490 ( 18) hydrogen bonds : angle 9.53637 ( 51) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 LYS cc_start: 0.7119 (mmtt) cc_final: 0.6867 (ttpp) REVERT: D 80 LYS cc_start: 0.8579 (ttpt) cc_final: 0.8058 (mttp) REVERT: I 70 VAL cc_start: 0.7119 (OUTLIER) cc_final: 0.6755 (t) outliers start: 27 outliers final: 24 residues processed: 121 average time/residue: 0.1705 time to fit residues: 27.2426 Evaluate side-chains 128 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 65 ASN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 34 optimal weight: 0.0170 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 1 optimal weight: 0.0870 chunk 26 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 50 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 = 0.5386 r_free = 0.5386 target = 0.251380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.5155 r_free = 0.5155 target = 0.192173 restraints weight = 25009.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.5249 r_free = 0.5249 target = 0.202640 restraints weight = 12210.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.5315 r_free = 0.5315 target = 0.210180 restraints weight = 7149.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.5357 r_free = 0.5357 target = 0.215374 restraints weight = 4609.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.5389 r_free = 0.5389 target = 0.219050 restraints weight = 3183.020| |-----------------------------------------------------------------------------| r_work (final): 0.5267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6286 moved from start: 0.7123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5496 Z= 0.097 Angle : 0.448 4.601 7416 Z= 0.260 Chirality : 0.053 0.377 984 Planarity : 0.001 0.007 924 Dihedral : 5.328 17.535 804 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 2.78 % Allowed : 28.33 % Favored : 68.89 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.00 (0.21), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.16), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR E 39 HIS 0.002 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 5496) covalent geometry : angle 0.44840 ( 7416) hydrogen bonds : bond 0.04688 ( 18) hydrogen bonds : angle 8.70084 ( 51) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 LYS cc_start: 0.6944 (mmtt) cc_final: 0.6611 (ttpp) REVERT: C 46 GLU cc_start: 0.8102 (pp20) cc_final: 0.7791 (pp20) REVERT: D 80 LYS cc_start: 0.8537 (ttpt) cc_final: 0.7997 (mttp) outliers start: 15 outliers final: 14 residues processed: 115 average time/residue: 0.1804 time to fit residues: 26.8788 Evaluate side-chains 117 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain K residue 65 ASN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 65 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 65 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 48 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 3 optimal weight: 0.0040 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 50 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 = 0.5354 r_free = 0.5354 target = 0.217280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5090 r_free = 0.5090 target = 0.187136 restraints weight = 22661.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.5170 r_free = 0.5170 target = 0.195774 restraints weight = 10886.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.5219 r_free = 0.5219 target = 0.201919 restraints weight = 6245.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.5248 r_free = 0.5248 target = 0.205804 restraints weight = 3912.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.5275 r_free = 0.5275 target = 0.208996 restraints weight = 2706.384| |-----------------------------------------------------------------------------| r_work (final): 0.5291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 moved from start: 0.7247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5496 Z= 0.091 Angle : 0.435 4.639 7416 Z= 0.252 Chirality : 0.053 0.380 984 Planarity : 0.001 0.007 924 Dihedral : 5.068 16.238 804 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 2.22 % Allowed : 29.26 % Favored : 68.52 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.87 (0.21), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.16), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR D 39 HIS 0.002 0.000 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 5496) covalent geometry : angle 0.43535 ( 7416) hydrogen bonds : bond 0.04326 ( 18) hydrogen bonds : angle 8.40813 ( 51) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2497.45 seconds wall clock time: 43 minutes 13.94 seconds (2593.94 seconds total)