Starting phenix.real_space_refine on Mon Jul 28 20:54:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ncj_12268/07_2025/7ncj_12268.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ncj_12268/07_2025/7ncj_12268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ncj_12268/07_2025/7ncj_12268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ncj_12268/07_2025/7ncj_12268.map" model { file = "/net/cci-nas-00/data/ceres_data/7ncj_12268/07_2025/7ncj_12268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ncj_12268/07_2025/7ncj_12268.cif" } resolution = 4.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 3294 2.51 5 N 924 2.21 5 O 1056 1.98 5 H 5586 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10860 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "B" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "C" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "D" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "E" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "F" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} 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: 5.43, per 1000 atoms: 0.50 Number of scatterers: 10860 At special positions: 0 Unit cell: (123.2, 78.1, 58.3, 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 1056 8.00 N 924 7.00 C 3294 6.00 H 5586 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: 2.70 Conformation dependent library (CDL) restraints added in 833.5 milliseconds 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1308 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 13 sheets defined 0.0% alpha, 40.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 56 removed outlier: 6.992A pdb=" N THR A 44 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LYS B 45 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL A 52 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA B 53 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR A 54 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL B 55 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA A 56 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N THR B 44 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LYS C 45 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL B 52 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ALA C 53 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N THR B 54 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL C 55 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ALA B 56 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N THR C 44 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LYS D 45 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL C 52 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA D 53 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR C 54 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL D 55 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ALA C 56 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N THR D 44 " --> pdb=" O LYS E 43 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LYS E 45 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL D 52 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ALA E 53 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR D 54 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL E 55 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ALA D 56 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR E 44 " --> pdb=" O LYS F 43 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LYS F 45 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL E 52 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ALA F 53 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR E 54 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL F 55 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA E 56 " --> pdb=" O VAL F 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 66 removed outlier: 6.799A pdb=" N GLU A 61 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N THR B 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL A 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL B 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASN A 65 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLU D 61 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N THR E 64 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL D 63 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL E 66 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASN D 65 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N THR F 64 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL E 63 " --> pdb=" O THR F 64 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N VAL F 66 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASN E 65 " --> pdb=" O VAL F 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 70 through 72 Processing sheet with id=AA5, first strand: chain 'A' and resid 75 through 83 removed outlier: 6.650A pdb=" N ALA B 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N GLN C 79 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA B 78 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N THR C 81 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS B 80 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N GLU C 83 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL B 82 " --> pdb=" O GLU C 83 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA C 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N GLN D 79 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA C 78 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N THR D 81 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LYS C 80 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N GLU D 83 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL C 82 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA D 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N GLN E 79 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA D 78 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N THR E 81 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LYS D 80 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N GLU E 83 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL D 82 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA E 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N GLN F 79 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA E 78 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N THR F 81 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS E 80 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N GLU F 83 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL E 82 " --> pdb=" O GLU F 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 88 through 89 Processing sheet with id=AA7, first strand: chain 'A' and resid 92 through 96 removed outlier: 6.994A pdb=" N GLY B 93 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLY C 93 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLY D 93 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLY E 93 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N PHE F 94 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL E 95 " --> pdb=" O PHE F 94 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LYS F 96 " --> pdb=" O VAL E 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 18 through 19 removed outlier: 7.193A pdb=" N ALA G 18 " --> pdb=" O ALA H 19 " (cutoff:3.500A) removed outlier: 9.448A pdb=" N LYS H 21 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA I 19 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS I 21 " --> pdb=" O GLU H 20 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 39 through 41 removed outlier: 5.823A pdb=" N TYR G 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY H 41 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N TYR I 39 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY J 41 " --> pdb=" O VAL K 40 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY K 41 " --> pdb=" O VAL L 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 49 through 55 removed outlier: 9.326A pdb=" N VAL G 49 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 10.672A pdb=" N VAL H 52 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLY G 51 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N THR H 54 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA G 53 " --> pdb=" O THR H 54 " (cutoff:3.500A) removed outlier: 9.276A pdb=" N VAL H 49 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 10.467A pdb=" N VAL I 52 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLY H 51 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N THR I 54 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA H 53 " --> pdb=" O THR I 54 " (cutoff:3.500A) removed outlier: 9.333A pdb=" N VAL I 49 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 10.596A pdb=" N VAL J 52 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLY I 51 " --> pdb=" O VAL J 52 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N THR J 54 " --> pdb=" O GLY I 51 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA I 53 " --> pdb=" O THR J 54 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N HIS J 50 " --> pdb=" O GLY K 51 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ALA K 53 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 9.051A pdb=" N VAL J 52 " --> pdb=" O ALA K 53 " (cutoff:3.500A) removed outlier: 10.814A pdb=" N VAL K 55 " --> pdb=" O VAL J 52 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N THR J 54 " --> pdb=" O VAL K 55 " (cutoff:3.500A) removed outlier: 9.193A pdb=" N HIS K 50 " --> pdb=" O GLY L 51 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ALA L 53 " --> pdb=" O HIS K 50 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N VAL K 52 " --> pdb=" O ALA L 53 " (cutoff:3.500A) removed outlier: 10.679A pdb=" N VAL L 55 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N THR K 54 " --> pdb=" O VAL L 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'G' and resid 63 through 66 removed outlier: 3.596A pdb=" N VAL H 66 " --> pdb=" O ASN G 65 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL I 66 " --> pdb=" O ASN H 65 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL J 66 " --> pdb=" O ASN I 65 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL K 66 " --> pdb=" O ASN J 65 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL L 66 " --> pdb=" O ASN K 65 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 85 through 88 removed outlier: 6.422A pdb=" N GLY H 86 " --> pdb=" O SER I 87 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLY I 86 " --> pdb=" O SER J 87 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N ALA J 89 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE I 88 " --> pdb=" O ALA J 89 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLY J 86 " --> pdb=" O SER K 87 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N ALA K 89 " --> pdb=" O GLY J 86 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE J 88 " --> pdb=" O ALA K 89 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLY K 86 " --> pdb=" O SER L 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'J' and resid 18 through 21 removed outlier: 3.796A pdb=" N ALA K 19 " --> pdb=" O ALA J 18 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS K 21 " --> pdb=" O GLU J 20 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA L 17 " --> pdb=" O VAL K 16 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS L 21 " --> pdb=" O GLU K 20 " (cutoff:3.500A) 105 hydrogen bonds defined for protein. 312 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.68 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 0.97: 4817 0.97 - 1.13: 769 1.13 - 1.28: 924 1.28 - 1.43: 1057 1.43 - 1.58: 3305 Bond restraints: 10872 Sorted by residual: bond pdb=" N VAL C 37 " pdb=" CA VAL C 37 " ideal model delta sigma weight residual 1.458 1.503 -0.045 1.90e-02 2.77e+03 5.68e+00 bond pdb=" N VAL B 37 " pdb=" CA VAL B 37 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.90e-02 2.77e+03 5.40e+00 bond pdb=" N VAL D 37 " pdb=" CA VAL D 37 " ideal model delta sigma weight residual 1.458 1.501 -0.043 1.90e-02 2.77e+03 5.20e+00 bond pdb=" N VAL F 37 " pdb=" CA VAL F 37 " ideal model delta sigma weight residual 1.458 1.501 -0.043 1.90e-02 2.77e+03 5.14e+00 bond pdb=" N LYS G 80 " pdb=" CA LYS G 80 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.54e-02 4.22e+03 5.05e+00 ... (remaining 10867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.10: 19765 7.10 - 14.19: 14 14.19 - 21.29: 0 21.29 - 28.39: 0 28.39 - 35.48: 3 Bond angle restraints: 19782 Sorted by residual: angle pdb=" N THR I 44 " pdb=" CA THR I 44 " pdb=" HA THR I 44 " ideal model delta sigma weight residual 110.00 74.52 35.48 3.00e+00 1.11e-01 1.40e+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 74.50 34.50 3.00e+00 1.11e-01 1.32e+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 80.41 28.59 3.00e+00 1.11e-01 9.09e+01 angle pdb=" C LYS I 58 " pdb=" N THR I 59 " pdb=" CA THR I 59 " ideal model delta sigma weight residual 122.99 131.30 -8.31 1.41e+00 5.03e-01 3.47e+01 angle pdb=" N THR G 81 " pdb=" CA THR G 81 " pdb=" C THR G 81 " ideal model delta sigma weight residual 111.40 118.18 -6.78 1.22e+00 6.72e-01 3.09e+01 ... (remaining 19777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 4297 17.99 - 35.99: 259 35.99 - 53.98: 139 53.98 - 71.97: 268 71.97 - 89.96: 11 Dihedral angle restraints: 4974 sinusoidal: 2784 harmonic: 2190 Sorted by residual: dihedral pdb=" CA SER G 87 " pdb=" C SER G 87 " pdb=" N ILE G 88 " pdb=" CA ILE G 88 " ideal model delta harmonic sigma weight residual 180.00 149.99 30.01 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA LYS I 80 " pdb=" C LYS I 80 " pdb=" N THR I 81 " pdb=" CA THR I 81 " ideal model delta harmonic sigma weight residual -180.00 -151.46 -28.54 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA LYS L 80 " pdb=" C LYS L 80 " pdb=" N THR L 81 " pdb=" CA THR L 81 " ideal model delta harmonic sigma weight residual 180.00 -151.68 -28.32 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 4971 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 695 0.106 - 0.211: 220 0.211 - 0.316: 27 0.316 - 0.421: 5 0.421 - 0.526: 1 Chirality restraints: 948 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 2.00 0.53 2.00e-01 2.50e+01 6.93e+00 chirality pdb=" CA GLU H 61 " pdb=" N GLU H 61 " pdb=" C GLU H 61 " pdb=" CB GLU H 61 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CA LYS E 60 " pdb=" N LYS E 60 " pdb=" C LYS E 60 " pdb=" CB LYS E 60 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 945 not shown) Planarity restraints: 1638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN L 62 " -0.031 2.00e-02 2.50e+03 4.73e-02 3.36e+01 pdb=" CD GLN L 62 " 0.004 2.00e-02 2.50e+03 pdb=" OE1 GLN L 62 " 0.012 2.00e-02 2.50e+03 pdb=" NE2 GLN L 62 " 0.084 2.00e-02 2.50e+03 pdb="HE21 GLN L 62 " 0.004 2.00e-02 2.50e+03 pdb="HE22 GLN L 62 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN H 62 " -0.032 2.00e-02 2.50e+03 4.67e-02 3.28e+01 pdb=" CD GLN H 62 " 0.006 2.00e-02 2.50e+03 pdb=" OE1 GLN H 62 " 0.012 2.00e-02 2.50e+03 pdb=" NE2 GLN H 62 " 0.081 2.00e-02 2.50e+03 pdb="HE21 GLN H 62 " 0.005 2.00e-02 2.50e+03 pdb="HE22 GLN H 62 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN J 62 " -0.028 2.00e-02 2.50e+03 4.01e-02 2.41e+01 pdb=" CD GLN J 62 " 0.008 2.00e-02 2.50e+03 pdb=" OE1 GLN J 62 " 0.009 2.00e-02 2.50e+03 pdb=" NE2 GLN J 62 " 0.069 2.00e-02 2.50e+03 pdb="HE21 GLN J 62 " 0.004 2.00e-02 2.50e+03 pdb="HE22 GLN J 62 " -0.062 2.00e-02 2.50e+03 ... (remaining 1635 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.23: 692 2.23 - 2.80: 21431 2.80 - 3.36: 25788 3.36 - 3.93: 33978 3.93 - 4.50: 50349 Nonbonded interactions: 132238 Sorted by model distance: nonbonded pdb=" HG SER G 87 " pdb=" O SER H 87 " model vdw 1.660 2.450 nonbonded pdb=" H THR I 44 " pdb=" HA THR I 44 " model vdw 1.664 1.816 nonbonded pdb=" HG SER K 87 " pdb=" O SER L 87 " model vdw 1.683 2.450 nonbonded pdb=" HG SER I 87 " pdb=" O SER J 87 " model vdw 1.702 2.450 nonbonded pdb=" HG SER H 87 " pdb=" O SER I 87 " model vdw 1.715 2.450 ... (remaining 132233 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 37 through 91) selection = (chain 'B' and resid 37 through 91) selection = (chain 'C' and resid 37 through 91) selection = (chain 'D' and resid 37 through 91) selection = (chain 'E' and resid 37 through 91) selection = (chain 'F' and resid 37 through 91) selection = (chain 'G' and resid 37 through 91) selection = (chain 'H' and resid 37 through 91) selection = (chain 'I' and resid 37 through 91) selection = (chain 'J' and resid 37 through 91) selection = (chain 'K' and resid 37 through 91) selection = (chain 'L' and resid 37 through 91) } 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: 0.920 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: 0.190 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.670 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5102 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 : 0.011 0.062 5286 Z= 0.611 Angle : 1.597 8.348 7140 Z= 0.955 Chirality : 0.100 0.526 948 Planarity : 0.006 0.026 882 Dihedral : 13.679 89.965 1782 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 0.18 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.72 % Favored : 92.01 % Rotamer: Outliers : 0.76 % Allowed : 2.65 % Favored : 96.59 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.22), residues: 738 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.17), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.027 0.009 HIS A 50 PHE 0.036 0.008 PHE E 94 TYR 0.047 0.011 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.22469 ( 105) hydrogen bonds : angle 9.66531 ( 312) covalent geometry : bond 0.01122 ( 5286) covalent geometry : angle 1.59694 ( 7140) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 205 time to evaluate : 0.735 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.4419 (t80) cc_final: 0.3934 (t80) REVERT: D 45 LYS cc_start: 0.6950 (mttt) cc_final: 0.6750 (mttt) REVERT: J 38 LEU cc_start: 0.5398 (tp) cc_final: 0.5053 (tp) REVERT: J 79 GLN cc_start: 0.4626 (OUTLIER) cc_final: 0.4104 (tp-100) outliers start: 4 outliers final: 0 residues processed: 209 average time/residue: 0.4635 time to fit residues: 118.3518 Evaluate side-chains 137 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 chunk 65 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 50 HIS ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.157795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.128194 restraints weight = 26157.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.137353 restraints weight = 12073.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.143112 restraints weight = 6594.734| |-----------------------------------------------------------------------------| r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5612 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5286 Z= 0.163 Angle : 0.652 4.379 7140 Z= 0.384 Chirality : 0.053 0.392 948 Planarity : 0.002 0.013 882 Dihedral : 7.156 22.520 768 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.23), residues: 738 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.17), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 50 PHE 0.013 0.003 PHE A 94 TYR 0.012 0.002 TYR A 39 Details of bonding type rmsd hydrogen bonds : bond 0.07612 ( 105) hydrogen bonds : angle 8.81518 ( 312) covalent geometry : bond 0.00326 ( 5286) covalent geometry : angle 0.65231 ( 7140) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.972 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.3726 (t80) cc_final: 0.3498 (t80) REVERT: B 39 TYR cc_start: 0.4005 (t80) cc_final: 0.3781 (t80) REVERT: D 88 ILE cc_start: 0.6736 (tt) cc_final: 0.6508 (pt) REVERT: G 45 LYS cc_start: 0.6781 (mmtp) cc_final: 0.6369 (mmtm) REVERT: H 45 LYS cc_start: 0.8798 (mttt) cc_final: 0.8265 (mtpt) REVERT: H 60 LYS cc_start: 0.8345 (mmtm) cc_final: 0.8122 (mmmt) REVERT: H 80 LYS cc_start: 0.8622 (ttpt) cc_final: 0.7827 (tptt) REVERT: I 60 LYS cc_start: 0.7955 (mttp) cc_final: 0.7696 (ttpt) REVERT: I 80 LYS cc_start: 0.8370 (ttpt) cc_final: 0.8146 (ptmt) REVERT: K 20 GLU cc_start: 0.7072 (mp0) cc_final: 0.6719 (mp0) REVERT: K 60 LYS cc_start: 0.7751 (ttmm) cc_final: 0.7494 (ttmm) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.5112 time to fit residues: 97.3948 Evaluate side-chains 139 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 45 optimal weight: 4.9990 chunk 69 optimal weight: 0.3980 chunk 29 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 32 optimal weight: 0.0980 chunk 14 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS A 79 GLN B 79 GLN C 50 HIS E 50 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.157297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.126804 restraints weight = 26235.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.136106 restraints weight = 12392.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.142214 restraints weight = 6869.423| |-----------------------------------------------------------------------------| r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5712 moved from start: 0.5671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5286 Z= 0.133 Angle : 0.554 5.221 7140 Z= 0.326 Chirality : 0.053 0.387 948 Planarity : 0.002 0.008 882 Dihedral : 6.240 18.964 768 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.24), residues: 738 helix: None (None), residues: 0 sheet: -0.19 (0.71), residues: 60 loop : -1.88 (0.18), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 PHE 0.018 0.002 PHE D 94 TYR 0.012 0.002 TYR L 39 Details of bonding type rmsd hydrogen bonds : bond 0.06530 ( 105) hydrogen bonds : angle 8.32064 ( 312) covalent geometry : bond 0.00270 ( 5286) covalent geometry : angle 0.55432 ( 7140) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.075 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 57 GLU cc_start: 0.7131 (pt0) cc_final: 0.6804 (pm20) REVERT: H 80 LYS cc_start: 0.8675 (ttpt) cc_final: 0.7968 (tptt) REVERT: I 60 LYS cc_start: 0.7893 (mttp) cc_final: 0.7640 (tttt) REVERT: I 80 LYS cc_start: 0.8487 (ttpt) cc_final: 0.8224 (ptmt) REVERT: J 21 LYS cc_start: 0.7422 (tmtt) cc_final: 0.7198 (tptp) REVERT: K 20 GLU cc_start: 0.6935 (mp0) cc_final: 0.6694 (mp0) REVERT: K 60 LYS cc_start: 0.7775 (ttmm) cc_final: 0.7479 (ttmm) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.6001 time to fit residues: 116.4444 Evaluate side-chains 131 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 21 optimal weight: 0.0870 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.4185 r_free = 0.4185 target = 0.145379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.116359 restraints weight = 26405.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.125103 restraints weight = 12136.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.130804 restraints weight = 6631.216| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5886 moved from start: 0.6668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5286 Z= 0.212 Angle : 0.617 5.958 7140 Z= 0.359 Chirality : 0.052 0.359 948 Planarity : 0.003 0.011 882 Dihedral : 6.415 20.819 768 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.23), residues: 738 helix: None (None), residues: 0 sheet: -0.76 (0.68), residues: 60 loop : -2.21 (0.18), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 50 PHE 0.010 0.002 PHE E 94 TYR 0.018 0.002 TYR L 39 Details of bonding type rmsd hydrogen bonds : bond 0.05805 ( 105) hydrogen bonds : angle 8.23646 ( 312) covalent geometry : bond 0.00421 ( 5286) covalent geometry : angle 0.61715 ( 7140) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.938 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 SER cc_start: 0.7454 (t) cc_final: 0.7062 (m) REVERT: B 46 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7570 (mm-30) REVERT: C 42 SER cc_start: 0.7982 (t) cc_final: 0.7507 (m) REVERT: C 45 LYS cc_start: 0.8245 (mttt) cc_final: 0.7810 (mtpp) REVERT: F 57 GLU cc_start: 0.7375 (pt0) cc_final: 0.6962 (pm20) REVERT: H 80 LYS cc_start: 0.8806 (ttpt) cc_final: 0.8155 (tptt) REVERT: I 60 LYS cc_start: 0.8030 (mttp) cc_final: 0.7718 (ttpt) REVERT: J 21 LYS cc_start: 0.7532 (tmtt) cc_final: 0.7249 (tptp) REVERT: J 65 ASN cc_start: 0.8778 (m-40) cc_final: 0.8528 (m-40) REVERT: K 20 GLU cc_start: 0.6842 (mp0) cc_final: 0.6565 (mp0) REVERT: K 60 LYS cc_start: 0.7819 (ttmm) cc_final: 0.7539 (ttmm) REVERT: K 80 LYS cc_start: 0.8779 (ttpt) cc_final: 0.8061 (tppt) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.6941 time to fit residues: 130.1652 Evaluate side-chains 129 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 11 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 0.0970 chunk 54 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.4187 r_free = 0.4187 target = 0.145177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.115748 restraints weight = 26295.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.124786 restraints weight = 11957.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.130784 restraints weight = 6471.596| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5880 moved from start: 0.7207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5286 Z= 0.150 Angle : 0.526 4.551 7140 Z= 0.307 Chirality : 0.052 0.382 948 Planarity : 0.002 0.007 882 Dihedral : 5.947 20.983 768 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.24), residues: 738 helix: None (None), residues: 0 sheet: -0.55 (0.72), residues: 60 loop : -2.11 (0.18), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 50 PHE 0.009 0.002 PHE B 94 TYR 0.012 0.002 TYR L 39 Details of bonding type rmsd hydrogen bonds : bond 0.05444 ( 105) hydrogen bonds : angle 7.98611 ( 312) covalent geometry : bond 0.00284 ( 5286) covalent geometry : angle 0.52589 ( 7140) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.958 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7441 (mm-30) REVERT: C 42 SER cc_start: 0.7983 (t) cc_final: 0.7622 (m) REVERT: E 39 TYR cc_start: 0.3881 (t80) cc_final: 0.3669 (t80) REVERT: F 57 GLU cc_start: 0.7199 (pt0) cc_final: 0.6779 (pm20) REVERT: F 88 ILE cc_start: 0.7462 (tt) cc_final: 0.7114 (pt) REVERT: H 80 LYS cc_start: 0.8740 (ttpt) cc_final: 0.8099 (tptt) REVERT: I 60 LYS cc_start: 0.8022 (mttp) cc_final: 0.7670 (ttpt) REVERT: I 65 ASN cc_start: 0.8722 (m-40) cc_final: 0.8503 (m-40) REVERT: I 80 LYS cc_start: 0.8651 (ptpt) cc_final: 0.8329 (ptmt) REVERT: J 21 LYS cc_start: 0.7564 (tmtt) cc_final: 0.7290 (tptp) REVERT: J 65 ASN cc_start: 0.8685 (m-40) cc_final: 0.8333 (m-40) REVERT: K 20 GLU cc_start: 0.6877 (mp0) cc_final: 0.6592 (mp0) REVERT: K 60 LYS cc_start: 0.7815 (ttmm) cc_final: 0.7546 (ttmm) REVERT: K 80 LYS cc_start: 0.8771 (ttpt) cc_final: 0.8031 (tppt) REVERT: L 80 LYS cc_start: 0.7584 (tptp) cc_final: 0.6841 (tppt) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.5071 time to fit residues: 97.2040 Evaluate side-chains 132 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 14 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 70 optimal weight: 0.1980 chunk 71 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 2 optimal weight: 0.0770 chunk 7 optimal weight: 3.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.4194 r_free = 0.4194 target = 0.145552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.115737 restraints weight = 26245.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.124864 restraints weight = 11882.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.130947 restraints weight = 6452.412| |-----------------------------------------------------------------------------| r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5873 moved from start: 0.7472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5286 Z= 0.118 Angle : 0.484 4.367 7140 Z= 0.284 Chirality : 0.052 0.373 948 Planarity : 0.002 0.012 882 Dihedral : 5.628 20.302 768 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.25), residues: 738 helix: None (None), residues: 0 sheet: -0.42 (0.75), residues: 60 loop : -2.02 (0.19), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 50 PHE 0.010 0.002 PHE D 94 TYR 0.010 0.001 TYR L 39 Details of bonding type rmsd hydrogen bonds : bond 0.05198 ( 105) hydrogen bonds : angle 7.67671 ( 312) covalent geometry : bond 0.00236 ( 5286) covalent geometry : angle 0.48448 ( 7140) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.813 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 LYS cc_start: 0.8256 (mttt) cc_final: 0.8030 (tttt) REVERT: D 60 LYS cc_start: 0.8446 (tttp) cc_final: 0.8199 (tmtt) REVERT: E 39 TYR cc_start: 0.3915 (t80) cc_final: 0.3624 (t80) REVERT: F 57 GLU cc_start: 0.7192 (pt0) cc_final: 0.6775 (pm20) REVERT: F 72 THR cc_start: 0.7462 (m) cc_final: 0.7202 (p) REVERT: H 80 LYS cc_start: 0.8762 (ttpt) cc_final: 0.8207 (tptt) REVERT: I 60 LYS cc_start: 0.8055 (mttp) cc_final: 0.7679 (ttpt) REVERT: I 65 ASN cc_start: 0.8705 (m-40) cc_final: 0.8486 (m-40) REVERT: J 21 LYS cc_start: 0.7583 (tmtt) cc_final: 0.7303 (tptp) REVERT: K 20 GLU cc_start: 0.6891 (mp0) cc_final: 0.6683 (mp0) REVERT: K 60 LYS cc_start: 0.7814 (ttmm) cc_final: 0.7476 (ttmm) REVERT: K 80 LYS cc_start: 0.8761 (ttpt) cc_final: 0.8019 (tppt) REVERT: L 80 LYS cc_start: 0.7600 (tptp) cc_final: 0.6884 (tppt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.4865 time to fit residues: 93.9069 Evaluate side-chains 137 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 31 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.4161 r_free = 0.4161 target = 0.142649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.113109 restraints weight = 26968.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.122228 restraints weight = 12067.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.128295 restraints weight = 6533.467| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5949 moved from start: 0.7927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5286 Z= 0.150 Angle : 0.516 6.127 7140 Z= 0.301 Chirality : 0.053 0.383 948 Planarity : 0.002 0.009 882 Dihedral : 5.678 20.062 768 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.25), residues: 738 helix: None (None), residues: 0 sheet: -0.71 (0.75), residues: 60 loop : -2.01 (0.19), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 50 PHE 0.014 0.002 PHE E 94 TYR 0.011 0.002 TYR I 39 Details of bonding type rmsd hydrogen bonds : bond 0.05018 ( 105) hydrogen bonds : angle 7.61252 ( 312) covalent geometry : bond 0.00292 ( 5286) covalent geometry : angle 0.51556 ( 7140) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.814 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 SER cc_start: 0.7487 (t) cc_final: 0.7142 (m) REVERT: B 46 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7211 (mm-30) REVERT: D 60 LYS cc_start: 0.8417 (tttp) cc_final: 0.8144 (tmtt) REVERT: E 57 GLU cc_start: 0.6469 (tt0) cc_final: 0.6218 (tt0) REVERT: F 88 ILE cc_start: 0.7481 (tt) cc_final: 0.7221 (pt) REVERT: I 60 LYS cc_start: 0.8138 (mttp) cc_final: 0.7768 (ttpt) REVERT: I 65 ASN cc_start: 0.8692 (m-40) cc_final: 0.8446 (m-40) REVERT: K 20 GLU cc_start: 0.6928 (mp0) cc_final: 0.6657 (mp0) REVERT: K 60 LYS cc_start: 0.7827 (ttmm) cc_final: 0.7490 (ttmm) REVERT: K 80 LYS cc_start: 0.8791 (ttpt) cc_final: 0.8016 (tppt) REVERT: L 80 LYS cc_start: 0.7727 (tptp) cc_final: 0.7006 (tppt) REVERT: L 83 GLU cc_start: 0.7195 (tp30) cc_final: 0.6953 (tp30) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.4802 time to fit residues: 95.4021 Evaluate side-chains 132 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 61 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 41 optimal weight: 0.0770 overall best weight: 0.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.4150 r_free = 0.4150 target = 0.140776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.111993 restraints weight = 26555.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.120969 restraints weight = 11797.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.126932 restraints weight = 6328.798| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5986 moved from start: 0.8300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5286 Z= 0.148 Angle : 0.493 5.179 7140 Z= 0.289 Chirality : 0.052 0.386 948 Planarity : 0.002 0.006 882 Dihedral : 5.593 21.293 768 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.26), residues: 738 helix: None (None), residues: 0 sheet: -0.81 (0.74), residues: 60 loop : -2.00 (0.20), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 50 PHE 0.008 0.002 PHE D 94 TYR 0.011 0.002 TYR I 39 Details of bonding type rmsd hydrogen bonds : bond 0.04832 ( 105) hydrogen bonds : angle 7.53994 ( 312) covalent geometry : bond 0.00292 ( 5286) covalent geometry : angle 0.49268 ( 7140) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.806 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7253 (mm-30) REVERT: D 60 LYS cc_start: 0.8422 (tttp) cc_final: 0.8156 (tmtt) REVERT: E 57 GLU cc_start: 0.6465 (tt0) cc_final: 0.6170 (tt0) REVERT: F 57 GLU cc_start: 0.7077 (pt0) cc_final: 0.6714 (pp20) REVERT: I 21 LYS cc_start: 0.7161 (tmtt) cc_final: 0.6947 (tptp) REVERT: I 60 LYS cc_start: 0.8219 (mttp) cc_final: 0.7845 (ttpt) REVERT: I 65 ASN cc_start: 0.8668 (m-40) cc_final: 0.8431 (m-40) REVERT: K 20 GLU cc_start: 0.6956 (mp0) cc_final: 0.6704 (mp0) REVERT: K 60 LYS cc_start: 0.7808 (ttmm) cc_final: 0.7545 (ttmm) REVERT: K 80 LYS cc_start: 0.8785 (ttpt) cc_final: 0.8014 (tppt) REVERT: L 80 LYS cc_start: 0.7749 (tptp) cc_final: 0.7001 (tppt) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.5222 time to fit residues: 101.8391 Evaluate side-chains 135 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 62 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 0.0870 chunk 41 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN J 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.138801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.111384 restraints weight = 24751.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.119731 restraints weight = 10940.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.125332 restraints weight = 5843.165| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6065 moved from start: 0.8649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5286 Z= 0.135 Angle : 0.482 4.355 7140 Z= 0.283 Chirality : 0.052 0.386 948 Planarity : 0.002 0.008 882 Dihedral : 5.488 21.791 768 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.26), residues: 738 helix: None (None), residues: 0 sheet: -0.91 (0.73), residues: 60 loop : -1.94 (0.20), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 50 PHE 0.009 0.002 PHE C 94 TYR 0.011 0.002 TYR B 39 Details of bonding type rmsd hydrogen bonds : bond 0.04766 ( 105) hydrogen bonds : angle 7.47145 ( 312) covalent geometry : bond 0.00265 ( 5286) covalent geometry : angle 0.48187 ( 7140) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.773 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 60 LYS cc_start: 0.8407 (tttp) cc_final: 0.8145 (tmtt) REVERT: E 57 GLU cc_start: 0.6343 (tt0) cc_final: 0.6106 (tt0) REVERT: F 57 GLU cc_start: 0.6723 (pt0) cc_final: 0.6523 (pm20) REVERT: H 80 LYS cc_start: 0.8743 (ttpt) cc_final: 0.8246 (tptt) REVERT: I 21 LYS cc_start: 0.7162 (tmtt) cc_final: 0.6950 (tptp) REVERT: I 60 LYS cc_start: 0.8116 (mttp) cc_final: 0.7804 (ttpt) REVERT: K 20 GLU cc_start: 0.6879 (mp0) cc_final: 0.6644 (mp0) REVERT: K 60 LYS cc_start: 0.7802 (ttmm) cc_final: 0.7534 (ttmm) REVERT: K 80 LYS cc_start: 0.8676 (ttpt) cc_final: 0.7951 (tppt) REVERT: L 80 LYS cc_start: 0.7694 (tptp) cc_final: 0.6962 (tppt) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.5676 time to fit residues: 109.8609 Evaluate side-chains 137 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 chunk 21 optimal weight: 0.0980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.4147 r_free = 0.4147 target = 0.139996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.112323 restraints weight = 26616.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.120975 restraints weight = 11914.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.126844 restraints weight = 6390.286| |-----------------------------------------------------------------------------| r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5990 moved from start: 0.8819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5286 Z= 0.118 Angle : 0.469 4.403 7140 Z= 0.273 Chirality : 0.052 0.384 948 Planarity : 0.002 0.015 882 Dihedral : 5.284 21.023 768 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.26), residues: 738 helix: None (None), residues: 0 sheet: -0.83 (0.74), residues: 60 loop : -1.87 (0.20), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 50 PHE 0.009 0.002 PHE C 94 TYR 0.009 0.001 TYR B 39 Details of bonding type rmsd hydrogen bonds : bond 0.04639 ( 105) hydrogen bonds : angle 7.38809 ( 312) covalent geometry : bond 0.00242 ( 5286) covalent geometry : angle 0.46900 ( 7140) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.752 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 LYS cc_start: 0.7669 (tttm) cc_final: 0.7459 (tmtt) REVERT: C 88 ILE cc_start: 0.6840 (mt) cc_final: 0.6582 (mt) REVERT: D 60 LYS cc_start: 0.8415 (tttp) cc_final: 0.8202 (tmtt) REVERT: E 39 TYR cc_start: 0.4145 (t80) cc_final: 0.3909 (t80) REVERT: E 57 GLU cc_start: 0.6596 (tt0) cc_final: 0.6328 (tt0) REVERT: F 57 GLU cc_start: 0.7062 (pt0) cc_final: 0.6735 (pm20) REVERT: H 80 LYS cc_start: 0.8796 (ttpt) cc_final: 0.8287 (tptt) REVERT: I 60 LYS cc_start: 0.8176 (mttp) cc_final: 0.7820 (ttpt) REVERT: K 60 LYS cc_start: 0.7802 (ttmm) cc_final: 0.7550 (ttmm) REVERT: K 80 LYS cc_start: 0.8747 (ttpt) cc_final: 0.8025 (tppt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.4887 time to fit residues: 94.0806 Evaluate side-chains 133 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 44 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 59 optimal weight: 0.0870 chunk 23 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.4143 r_free = 0.4143 target = 0.139251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.110956 restraints weight = 26645.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.119809 restraints weight = 11831.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.125840 restraints weight = 6342.380| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6011 moved from start: 0.9005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5286 Z= 0.124 Angle : 0.470 4.285 7140 Z= 0.275 Chirality : 0.052 0.388 948 Planarity : 0.002 0.009 882 Dihedral : 5.260 20.878 768 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.26), residues: 738 helix: None (None), residues: 0 sheet: -0.96 (0.73), residues: 60 loop : -1.86 (0.20), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS A 50 PHE 0.009 0.002 PHE C 94 TYR 0.013 0.002 TYR H 39 Details of bonding type rmsd hydrogen bonds : bond 0.04633 ( 105) hydrogen bonds : angle 7.31039 ( 312) covalent geometry : bond 0.00247 ( 5286) covalent geometry : angle 0.46958 ( 7140) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5365.53 seconds wall clock time: 95 minutes 57.51 seconds (5757.51 seconds total)