Starting phenix.real_space_refine on Wed Mar 4 04:01:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ncj_12268/03_2026/7ncj_12268.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ncj_12268/03_2026/7ncj_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_12268/03_2026/7ncj_12268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ncj_12268/03_2026/7ncj_12268.map" model { file = "/net/cci-nas-00/data/ceres_data/7ncj_12268/03_2026/7ncj_12268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ncj_12268/03_2026/7ncj_12268.cif" } resolution = 4.23 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 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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.00, per 1000 atoms: 0.18 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: 0.86 Conformation dependent library (CDL) restraints added in 442.6 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: 0.35 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: 2.20 Time building geometry restraints manager: 1.23 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: 0.00 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: 1.020 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: 0.070 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.540 Find NCS groups from input model: 0.160 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.390 ------------------------------------------------------------------------------- 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 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: -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 TYR 0.047 0.011 TYR E 39 PHE 0.036 0.008 PHE E 94 HIS 0.027 0.009 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.01122 ( 5286) covalent geometry : angle 1.59694 ( 7140) hydrogen bonds : bond 0.22469 ( 105) hydrogen bonds : angle 9.66531 ( 312) *********************** 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 : 0.271 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: 0.5397 (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: 0.2157 time to fit residues: 54.9904 Evaluate side-chains 135 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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: 2.9990 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4301 r_free = 0.4301 target = 0.158335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.128081 restraints weight = 26386.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.137455 restraints weight = 12037.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.143585 restraints weight = 6539.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.147563 restraints weight = 3957.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.150175 restraints weight = 2597.497| |-----------------------------------------------------------------------------| r_work (final): 0.4254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5549 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5286 Z= 0.156 Angle : 0.638 4.576 7140 Z= 0.375 Chirality : 0.053 0.387 948 Planarity : 0.002 0.010 882 Dihedral : 7.174 22.585 768 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Cbeta Deviations : 0.15 % 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: -2.59 (0.22), 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 TYR 0.012 0.002 TYR A 39 PHE 0.011 0.003 PHE A 94 HIS 0.004 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 5286) covalent geometry : angle 0.63754 ( 7140) hydrogen bonds : bond 0.07509 ( 105) hydrogen bonds : angle 8.81336 ( 312) *********************** 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 159 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.270 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: A 39 TYR cc_start: 0.3714 (t80) cc_final: 0.3454 (t80) REVERT: B 39 TYR cc_start: 0.3962 (t80) cc_final: 0.3551 (t80) REVERT: D 88 ILE cc_start: 0.6653 (tt) cc_final: 0.6432 (pt) REVERT: G 45 LYS cc_start: 0.6763 (mmtp) cc_final: 0.6359 (mmtm) REVERT: H 45 LYS cc_start: 0.8789 (mttt) cc_final: 0.8280 (mtpt) REVERT: H 80 LYS cc_start: 0.8607 (ttpt) cc_final: 0.7824 (tptt) REVERT: I 80 LYS cc_start: 0.8336 (ttpt) cc_final: 0.8116 (ptmt) REVERT: K 20 GLU cc_start: 0.7066 (mp0) cc_final: 0.6742 (mp0) REVERT: K 60 LYS cc_start: 0.7708 (ttmm) cc_final: 0.7441 (ttmm) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2254 time to fit residues: 43.2289 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 : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 2 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 0.0770 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.9742 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS E 50 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.156808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.126333 restraints weight = 26209.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.135268 restraints weight = 12457.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.141206 restraints weight = 6958.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.145020 restraints weight = 4315.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.147683 restraints weight = 2918.307| |-----------------------------------------------------------------------------| r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5717 moved from start: 0.5722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 5286 Z= 0.162 Angle : 0.583 5.486 7140 Z= 0.344 Chirality : 0.053 0.387 948 Planarity : 0.002 0.009 882 Dihedral : 6.503 19.960 768 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Cbeta Deviations : 0.15 % 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: -2.47 (0.24), residues: 738 helix: None (None), residues: 0 sheet: -0.44 (0.69), residues: 60 loop : -1.98 (0.18), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.002 TYR C 39 PHE 0.020 0.002 PHE D 94 HIS 0.003 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 5286) covalent geometry : angle 0.58333 ( 7140) hydrogen bonds : bond 0.06748 ( 105) hydrogen bonds : angle 8.48768 ( 312) *********************** 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 155 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.238 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: D 88 ILE cc_start: 0.6829 (tt) cc_final: 0.6602 (pt) REVERT: E 39 TYR cc_start: 0.3695 (t80) cc_final: 0.3444 (t80) REVERT: F 57 GLU cc_start: 0.7002 (pt0) cc_final: 0.6619 (pm20) REVERT: H 46 GLU cc_start: 0.7866 (pm20) cc_final: 0.7574 (pp20) REVERT: H 80 LYS cc_start: 0.8644 (ttpt) cc_final: 0.7956 (tptt) REVERT: I 80 LYS cc_start: 0.8440 (ttpt) cc_final: 0.8188 (ptmt) REVERT: J 21 LYS cc_start: 0.7423 (tmtt) cc_final: 0.7189 (tptp) REVERT: K 20 GLU cc_start: 0.6942 (mp0) cc_final: 0.6691 (mp0) REVERT: K 38 LEU cc_start: 0.7112 (mt) cc_final: 0.6882 (mt) REVERT: K 60 LYS cc_start: 0.7755 (ttmm) cc_final: 0.7443 (ttmm) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.2234 time to fit residues: 41.9401 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 : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.143458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.114505 restraints weight = 26705.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.123215 restraints weight = 12259.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.128965 restraints weight = 6719.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.132734 restraints weight = 4095.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.135140 restraints weight = 2699.517| |-----------------------------------------------------------------------------| r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5849 moved from start: 0.6792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 5286 Z= 0.224 Angle : 0.632 6.863 7140 Z= 0.368 Chirality : 0.052 0.390 948 Planarity : 0.003 0.010 882 Dihedral : 6.593 21.569 768 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Cbeta Deviations : 0.15 % 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: -2.85 (0.23), residues: 738 helix: None (None), residues: 0 sheet: -0.85 (0.67), residues: 60 loop : -2.24 (0.18), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.002 TYR L 39 PHE 0.009 0.002 PHE E 94 HIS 0.008 0.002 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 5286) covalent geometry : angle 0.63230 ( 7140) hydrogen bonds : bond 0.05898 ( 105) hydrogen bonds : angle 8.30085 ( 312) *********************** 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 152 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.260 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: B 42 SER cc_start: 0.7404 (t) cc_final: 0.6993 (m) REVERT: C 42 SER cc_start: 0.7947 (t) cc_final: 0.7481 (m) REVERT: D 45 LYS cc_start: 0.7629 (mttt) cc_final: 0.7277 (mttt) REVERT: F 57 GLU cc_start: 0.7262 (pt0) cc_final: 0.6833 (pm20) REVERT: H 80 LYS cc_start: 0.8805 (ttpt) cc_final: 0.8152 (tptt) REVERT: J 65 ASN cc_start: 0.8763 (m-40) cc_final: 0.8516 (m-40) REVERT: K 20 GLU cc_start: 0.6850 (mp0) cc_final: 0.5868 (mp0) REVERT: K 60 LYS cc_start: 0.7797 (ttmm) cc_final: 0.7502 (ttmm) REVERT: K 80 LYS cc_start: 0.8751 (ttpt) cc_final: 0.8035 (tppt) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.2313 time to fit residues: 42.2853 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 : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 28 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.139175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.112327 restraints weight = 24229.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.120646 restraints weight = 10958.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.126083 restraints weight = 5885.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.129582 restraints weight = 3527.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.131684 restraints weight = 2288.059| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5977 moved from start: 0.7441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5286 Z= 0.187 Angle : 0.579 4.941 7140 Z= 0.336 Chirality : 0.053 0.380 948 Planarity : 0.002 0.011 882 Dihedral : 6.335 22.187 768 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % 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 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: -2.77 (0.24), residues: 738 helix: None (None), residues: 0 sheet: -0.84 (0.72), residues: 60 loop : -2.18 (0.19), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.003 TYR B 39 PHE 0.008 0.001 PHE D 94 HIS 0.005 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 5286) covalent geometry : angle 0.57874 ( 7140) hydrogen bonds : bond 0.05719 ( 105) hydrogen bonds : angle 8.18171 ( 312) *********************** 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 155 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.178 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: B 42 SER cc_start: 0.7245 (t) cc_final: 0.6989 (m) REVERT: C 46 GLU cc_start: 0.7881 (tp30) cc_final: 0.7541 (tp30) REVERT: D 45 LYS cc_start: 0.7645 (mttt) cc_final: 0.7234 (mttt) REVERT: F 57 GLU cc_start: 0.6681 (pt0) cc_final: 0.6411 (pm20) REVERT: H 80 LYS cc_start: 0.8609 (ttpt) cc_final: 0.8018 (tptt) REVERT: I 46 GLU cc_start: 0.7680 (pp20) cc_final: 0.7421 (pp20) REVERT: I 80 LYS cc_start: 0.8653 (ptpt) cc_final: 0.8302 (ptmt) REVERT: J 65 ASN cc_start: 0.8474 (m-40) cc_final: 0.8257 (m-40) REVERT: K 60 LYS cc_start: 0.7753 (ttmm) cc_final: 0.7465 (ttmm) REVERT: K 80 LYS cc_start: 0.8589 (ttpt) cc_final: 0.7904 (tppt) REVERT: L 80 LYS cc_start: 0.7421 (tptp) cc_final: 0.6786 (tppt) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.2137 time to fit residues: 40.2495 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 : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 55 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.0670 chunk 51 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.6920 ------------------------------------------------------------------------------- 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 = 0.4149 r_free = 0.4149 target = 0.141981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.112807 restraints weight = 26362.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.121787 restraints weight = 11842.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.127691 restraints weight = 6378.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.131423 restraints weight = 3841.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.134076 restraints weight = 2525.538| |-----------------------------------------------------------------------------| r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5871 moved from start: 0.7802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5286 Z= 0.130 Angle : 0.508 4.903 7140 Z= 0.296 Chirality : 0.052 0.384 948 Planarity : 0.002 0.016 882 Dihedral : 5.830 21.172 768 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.84 % Favored : 89.16 % 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 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: -2.59 (0.25), residues: 738 helix: None (None), residues: 0 sheet: -0.78 (0.74), residues: 60 loop : -2.04 (0.19), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR L 39 PHE 0.009 0.002 PHE D 94 HIS 0.002 0.000 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 5286) covalent geometry : angle 0.50849 ( 7140) hydrogen bonds : bond 0.05187 ( 105) hydrogen bonds : angle 7.86164 ( 312) *********************** 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 165 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.193 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: B 42 SER cc_start: 0.7548 (t) cc_final: 0.7109 (m) REVERT: D 45 LYS cc_start: 0.7701 (mttt) cc_final: 0.7352 (mttt) REVERT: E 45 LYS cc_start: 0.8221 (tptm) cc_final: 0.7910 (mtpp) REVERT: F 57 GLU cc_start: 0.7035 (pt0) cc_final: 0.6661 (pm20) REVERT: F 72 THR cc_start: 0.7101 (m) cc_final: 0.6874 (p) REVERT: H 80 LYS cc_start: 0.8759 (ttpt) cc_final: 0.8241 (tptt) REVERT: I 21 LYS cc_start: 0.7250 (tmtt) cc_final: 0.7021 (tmtt) REVERT: J 65 ASN cc_start: 0.8629 (m-40) cc_final: 0.8276 (m-40) REVERT: K 20 GLU cc_start: 0.6664 (mp0) cc_final: 0.6420 (mp0) REVERT: K 60 LYS cc_start: 0.7779 (ttmm) cc_final: 0.7496 (ttmm) REVERT: K 80 LYS cc_start: 0.8724 (ttpt) cc_final: 0.7958 (tppt) REVERT: L 20 GLU cc_start: 0.4973 (mp0) cc_final: 0.4724 (mp0) REVERT: L 80 LYS cc_start: 0.7552 (tptp) cc_final: 0.6889 (tppt) REVERT: L 83 GLU cc_start: 0.7052 (tp30) cc_final: 0.6836 (tp30) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2161 time to fit residues: 43.4083 Evaluate side-chains 138 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 16 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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** ** A 79 GLN ** 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** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN ** L 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.139676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.110533 restraints weight = 27954.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.118645 restraints weight = 13109.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.124182 restraints weight = 7421.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.127745 restraints weight = 4691.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.130352 restraints weight = 3251.476| |-----------------------------------------------------------------------------| r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6095 moved from start: 0.8504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 5286 Z= 0.242 Angle : 0.623 4.328 7140 Z= 0.364 Chirality : 0.053 0.394 948 Planarity : 0.003 0.009 882 Dihedral : 6.537 22.568 768 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Cbeta Deviations : 0.15 % 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: -3.04 (0.24), residues: 738 helix: None (None), residues: 0 sheet: -1.32 (0.71), residues: 60 loop : -2.35 (0.18), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.002 TYR I 39 PHE 0.008 0.002 PHE B 94 HIS 0.006 0.002 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 5286) covalent geometry : angle 0.62276 ( 7140) hydrogen bonds : bond 0.05364 ( 105) hydrogen bonds : angle 7.90449 ( 312) *********************** 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 156 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.261 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: D 45 LYS cc_start: 0.7825 (mttt) cc_final: 0.7504 (mttt) REVERT: D 60 LYS cc_start: 0.8301 (tttp) cc_final: 0.8025 (tmtt) REVERT: E 45 LYS cc_start: 0.8276 (tptm) cc_final: 0.8017 (mtpp) REVERT: E 57 GLU cc_start: 0.6622 (tt0) cc_final: 0.6322 (tt0) REVERT: H 65 ASN cc_start: 0.8417 (m-40) cc_final: 0.8168 (m-40) REVERT: I 65 ASN cc_start: 0.8765 (m-40) cc_final: 0.8509 (m-40) REVERT: J 21 LYS cc_start: 0.7601 (tmtt) cc_final: 0.7314 (tptp) REVERT: K 60 LYS cc_start: 0.7779 (ttmm) cc_final: 0.7501 (ttmm) REVERT: K 80 LYS cc_start: 0.8650 (ttpt) cc_final: 0.7928 (tppt) REVERT: L 80 LYS cc_start: 0.7637 (tptp) cc_final: 0.6863 (tppt) REVERT: L 83 GLU cc_start: 0.7470 (tp30) cc_final: 0.7034 (tp30) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.2354 time to fit residues: 44.1383 Evaluate side-chains 136 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 43 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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** ** G 65 ASN ** 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 = 0.4211 r_free = 0.4211 target = 0.141207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.112128 restraints weight = 27759.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.120343 restraints weight = 12997.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.125902 restraints weight = 7257.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.129704 restraints weight = 4570.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.132236 restraints weight = 3080.869| |-----------------------------------------------------------------------------| r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 0.8719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5286 Z= 0.145 Angle : 0.515 4.187 7140 Z= 0.301 Chirality : 0.053 0.388 948 Planarity : 0.002 0.007 882 Dihedral : 5.940 23.056 768 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % 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 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: -2.81 (0.25), residues: 738 helix: None (None), residues: 0 sheet: -1.04 (0.74), residues: 60 loop : -2.19 (0.19), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR I 39 PHE 0.007 0.002 PHE B 94 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 5286) covalent geometry : angle 0.51491 ( 7140) hydrogen bonds : bond 0.05251 ( 105) hydrogen bonds : angle 7.75667 ( 312) *********************** 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 165 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.317 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: D 45 LYS cc_start: 0.7770 (mttt) cc_final: 0.7472 (mttt) REVERT: D 60 LYS cc_start: 0.8367 (tttp) cc_final: 0.8089 (tmtt) REVERT: E 45 LYS cc_start: 0.8272 (tptm) cc_final: 0.7993 (mtpp) REVERT: E 57 GLU cc_start: 0.6606 (tt0) cc_final: 0.6373 (tt0) REVERT: H 46 GLU cc_start: 0.7099 (pp20) cc_final: 0.6512 (pp20) REVERT: I 21 LYS cc_start: 0.7340 (tmtt) cc_final: 0.7042 (tmtt) REVERT: K 20 GLU cc_start: 0.6622 (mp0) cc_final: 0.6267 (mp0) REVERT: K 60 LYS cc_start: 0.7745 (ttmm) cc_final: 0.7470 (ttmm) REVERT: K 80 LYS cc_start: 0.8606 (ttpt) cc_final: 0.7908 (tppt) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2254 time to fit residues: 45.0492 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 : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 0.0870 chunk 6 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- 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** ** A 79 GLN ** 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** ** G 65 ASN ** 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 = 0.4132 r_free = 0.4132 target = 0.139610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.110552 restraints weight = 27432.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.119321 restraints weight = 12508.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.125259 restraints weight = 6868.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.129037 restraints weight = 4202.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.131706 restraints weight = 2794.674| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6003 moved from start: 0.8962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5286 Z= 0.135 Angle : 0.508 4.471 7140 Z= 0.293 Chirality : 0.053 0.390 948 Planarity : 0.002 0.014 882 Dihedral : 5.748 22.263 768 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % 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 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: -2.65 (0.26), residues: 738 helix: None (None), residues: 0 sheet: -1.07 (0.73), residues: 60 loop : -2.06 (0.20), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR L 39 PHE 0.008 0.002 PHE D 94 HIS 0.002 0.000 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 5286) covalent geometry : angle 0.50770 ( 7140) hydrogen bonds : bond 0.05087 ( 105) hydrogen bonds : angle 7.61748 ( 312) *********************** 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 160 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.203 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: D 45 LYS cc_start: 0.7773 (mttt) cc_final: 0.7479 (mttt) REVERT: D 60 LYS cc_start: 0.8422 (tttp) cc_final: 0.8190 (tmtt) REVERT: E 45 LYS cc_start: 0.8327 (tptm) cc_final: 0.8035 (mtpp) REVERT: E 57 GLU cc_start: 0.6657 (tt0) cc_final: 0.6412 (tt0) REVERT: E 60 LYS cc_start: 0.7297 (mttt) cc_final: 0.6881 (mmtm) REVERT: F 57 GLU cc_start: 0.7005 (pt0) cc_final: 0.6695 (pm20) REVERT: H 65 ASN cc_start: 0.8398 (m-40) cc_final: 0.8185 (m-40) REVERT: H 80 LYS cc_start: 0.8811 (ttpt) cc_final: 0.8292 (tptt) REVERT: I 21 LYS cc_start: 0.7282 (tmtt) cc_final: 0.6985 (tmtt) REVERT: K 60 LYS cc_start: 0.7747 (ttmm) cc_final: 0.7476 (ttmm) REVERT: K 80 LYS cc_start: 0.8647 (ttpt) cc_final: 0.7897 (tppt) REVERT: L 38 LEU cc_start: 0.7369 (pp) cc_final: 0.7104 (mt) REVERT: L 80 LYS cc_start: 0.7607 (tptp) cc_final: 0.7146 (tppt) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2300 time to fit residues: 44.3156 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 : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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** ** A 79 GLN ** 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** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** 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 = 0.4039 r_free = 0.4039 target = 0.130901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.104122 restraints weight = 25216.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.112106 restraints weight = 11117.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.117469 restraints weight = 5959.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.120801 restraints weight = 3595.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.123253 restraints weight = 2414.793| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6171 moved from start: 0.9599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5286 Z= 0.225 Angle : 0.601 4.306 7140 Z= 0.349 Chirality : 0.053 0.390 948 Planarity : 0.003 0.013 882 Dihedral : 6.508 23.033 768 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % 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 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: -3.05 (0.25), residues: 738 helix: None (None), residues: 0 sheet: -1.79 (0.66), residues: 60 loop : -2.30 (0.19), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR L 39 PHE 0.009 0.002 PHE F 94 HIS 0.005 0.002 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 5286) covalent geometry : angle 0.60109 ( 7140) hydrogen bonds : bond 0.05360 ( 105) hydrogen bonds : angle 7.80425 ( 312) ********************** 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 155 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.237 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: D 45 LYS cc_start: 0.7819 (mttt) cc_final: 0.7508 (mttt) REVERT: D 60 LYS cc_start: 0.8278 (tttp) cc_final: 0.8016 (tmtt) REVERT: E 45 LYS cc_start: 0.8269 (tptm) cc_final: 0.7989 (mtpp) REVERT: E 79 GLN cc_start: 0.7415 (tt0) cc_final: 0.6969 (tp40) REVERT: H 65 ASN cc_start: 0.8372 (m-40) cc_final: 0.8078 (m-40) REVERT: H 80 LYS cc_start: 0.8739 (ttpt) cc_final: 0.8312 (tptt) REVERT: K 20 GLU cc_start: 0.6621 (mp0) cc_final: 0.6362 (mp0) REVERT: K 60 LYS cc_start: 0.7783 (ttmm) cc_final: 0.7439 (ttmm) REVERT: K 80 LYS cc_start: 0.8453 (ttpt) cc_final: 0.7751 (tppt) REVERT: L 83 GLU cc_start: 0.7778 (tp30) cc_final: 0.7567 (tp30) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.2266 time to fit residues: 42.6001 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 : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 45 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 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** E 65 ASN G 65 ASN ** L 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.136010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.109488 restraints weight = 25053.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.117269 restraints weight = 11260.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.122297 restraints weight = 6025.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.125763 restraints weight = 3677.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.128152 restraints weight = 2420.135| |-----------------------------------------------------------------------------| r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6161 moved from start: 0.9725 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= 0.135 Angle : 0.516 4.409 7140 Z= 0.300 Chirality : 0.052 0.388 948 Planarity : 0.002 0.010 882 Dihedral : 5.898 22.668 768 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.38 % Favored : 88.62 % 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 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: -2.80 (0.26), residues: 738 helix: None (None), residues: 0 sheet: -1.50 (0.69), residues: 60 loop : -2.13 (0.20), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR I 39 PHE 0.009 0.002 PHE B 94 HIS 0.002 0.000 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 5286) covalent geometry : angle 0.51631 ( 7140) hydrogen bonds : bond 0.05126 ( 105) hydrogen bonds : angle 7.60631 ( 312) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2418.54 seconds wall clock time: 41 minutes 45.83 seconds (2505.83 seconds total)