Starting phenix.real_space_refine on Fri Feb 14 21:49:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ncj_12268/02_2025/7ncj_12268.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ncj_12268/02_2025/7ncj_12268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ncj_12268/02_2025/7ncj_12268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ncj_12268/02_2025/7ncj_12268.map" model { file = "/net/cci-nas-00/data/ceres_data/7ncj_12268/02_2025/7ncj_12268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ncj_12268/02_2025/7ncj_12268.cif" } resolution = 4.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians C 3294 2.51 5 N 924 2.21 5 O 1056 1.98 5 H 5586 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10860 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "B" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "C" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "D" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "E" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "F" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "G" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "I" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "J" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "K" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "L" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Time building chain proxies: 5.23, per 1000 atoms: 0.48 Number of scatterers: 10860 At special positions: 0 Unit cell: (123.2, 78.1, 58.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 1056 8.00 N 924 7.00 C 3294 6.00 H 5586 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.69 Conformation dependent library (CDL) restraints added in 770.7 milliseconds 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1308 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 13 sheets defined 0.0% alpha, 40.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 56 removed outlier: 6.992A pdb=" N THR A 44 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LYS B 45 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL A 52 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA B 53 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR A 54 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL B 55 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA A 56 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N THR B 44 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LYS C 45 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL B 52 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ALA C 53 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N THR B 54 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL C 55 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ALA B 56 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N THR C 44 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LYS D 45 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL C 52 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA D 53 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR C 54 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL D 55 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ALA C 56 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N THR D 44 " --> pdb=" O LYS E 43 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LYS E 45 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL D 52 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ALA E 53 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR D 54 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL E 55 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ALA D 56 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR E 44 " --> pdb=" O LYS F 43 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LYS F 45 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL E 52 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ALA F 53 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR E 54 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL F 55 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA E 56 " --> pdb=" O VAL F 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 66 removed outlier: 6.799A pdb=" N GLU A 61 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N THR B 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL A 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL B 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASN A 65 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLU D 61 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N THR E 64 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL D 63 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL E 66 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASN D 65 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N THR F 64 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL E 63 " --> pdb=" O THR F 64 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N VAL F 66 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASN E 65 " --> pdb=" O VAL F 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 70 through 72 Processing sheet with id=AA5, first strand: chain 'A' and resid 75 through 83 removed outlier: 6.650A pdb=" N ALA B 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N GLN C 79 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA B 78 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N THR C 81 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS B 80 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N GLU C 83 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL B 82 " --> pdb=" O GLU C 83 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA C 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N GLN D 79 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA C 78 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N THR D 81 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LYS C 80 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N GLU D 83 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL C 82 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA D 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N GLN E 79 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA D 78 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N THR E 81 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LYS D 80 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N GLU E 83 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL D 82 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA E 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N GLN F 79 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA E 78 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N THR F 81 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS E 80 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N GLU F 83 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL E 82 " --> pdb=" O GLU F 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 88 through 89 Processing sheet with id=AA7, first strand: chain 'A' and resid 92 through 96 removed outlier: 6.994A pdb=" N GLY B 93 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLY C 93 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLY D 93 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLY E 93 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N PHE F 94 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL E 95 " --> pdb=" O PHE F 94 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LYS F 96 " --> pdb=" O VAL E 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 18 through 19 removed outlier: 7.193A pdb=" N ALA G 18 " --> pdb=" O ALA H 19 " (cutoff:3.500A) removed outlier: 9.448A pdb=" N LYS H 21 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA I 19 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS I 21 " --> pdb=" O GLU H 20 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 39 through 41 removed outlier: 5.823A pdb=" N TYR G 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY H 41 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N TYR I 39 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY J 41 " --> pdb=" O VAL K 40 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY K 41 " --> pdb=" O VAL L 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 49 through 55 removed outlier: 9.326A pdb=" N VAL G 49 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 10.672A pdb=" N VAL H 52 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLY G 51 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N THR H 54 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA G 53 " --> pdb=" O THR H 54 " (cutoff:3.500A) removed outlier: 9.276A pdb=" N VAL H 49 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 10.467A pdb=" N VAL I 52 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLY H 51 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N THR I 54 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA H 53 " --> pdb=" O THR I 54 " (cutoff:3.500A) removed outlier: 9.333A pdb=" N VAL I 49 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 10.596A pdb=" N VAL J 52 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLY I 51 " --> pdb=" O VAL J 52 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N THR J 54 " --> pdb=" O GLY I 51 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA I 53 " --> pdb=" O THR J 54 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N HIS J 50 " --> pdb=" O GLY K 51 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ALA K 53 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 9.051A pdb=" N VAL J 52 " --> pdb=" O ALA K 53 " (cutoff:3.500A) removed outlier: 10.814A pdb=" N VAL K 55 " --> pdb=" O VAL J 52 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N THR J 54 " --> pdb=" O VAL K 55 " (cutoff:3.500A) removed outlier: 9.193A pdb=" N HIS K 50 " --> pdb=" O GLY L 51 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ALA L 53 " --> pdb=" O HIS K 50 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N VAL K 52 " --> pdb=" O ALA L 53 " (cutoff:3.500A) removed outlier: 10.679A pdb=" N VAL L 55 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N THR K 54 " --> pdb=" O VAL L 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'G' and resid 63 through 66 removed outlier: 3.596A pdb=" N VAL H 66 " --> pdb=" O ASN G 65 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL I 66 " --> pdb=" O ASN H 65 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL J 66 " --> pdb=" O ASN I 65 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL K 66 " --> pdb=" O ASN J 65 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL L 66 " --> pdb=" O ASN K 65 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 85 through 88 removed outlier: 6.422A pdb=" N GLY H 86 " --> pdb=" O SER I 87 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLY I 86 " --> pdb=" O SER J 87 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N ALA J 89 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE I 88 " --> pdb=" O ALA J 89 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLY J 86 " --> pdb=" O SER K 87 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N ALA K 89 " --> pdb=" O GLY J 86 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE J 88 " --> pdb=" O ALA K 89 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLY K 86 " --> pdb=" O SER L 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'J' and resid 18 through 21 removed outlier: 3.796A pdb=" N ALA K 19 " --> pdb=" O ALA J 18 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS K 21 " --> pdb=" O GLU J 20 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA L 17 " --> pdb=" O VAL K 16 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS L 21 " --> pdb=" O GLU K 20 " (cutoff:3.500A) 105 hydrogen bonds defined for protein. 312 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.99 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 0.97: 4817 0.97 - 1.13: 769 1.13 - 1.28: 924 1.28 - 1.43: 1057 1.43 - 1.58: 3305 Bond restraints: 10872 Sorted by residual: bond pdb=" N VAL C 37 " pdb=" CA VAL C 37 " ideal model delta sigma weight residual 1.458 1.503 -0.045 1.90e-02 2.77e+03 5.68e+00 bond pdb=" N VAL B 37 " pdb=" CA VAL B 37 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.90e-02 2.77e+03 5.40e+00 bond pdb=" N VAL D 37 " pdb=" CA VAL D 37 " ideal model delta sigma weight residual 1.458 1.501 -0.043 1.90e-02 2.77e+03 5.20e+00 bond pdb=" N VAL F 37 " pdb=" CA VAL F 37 " ideal model delta sigma weight residual 1.458 1.501 -0.043 1.90e-02 2.77e+03 5.14e+00 bond pdb=" N LYS G 80 " pdb=" CA LYS G 80 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.54e-02 4.22e+03 5.05e+00 ... (remaining 10867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.10: 19765 7.10 - 14.19: 14 14.19 - 21.29: 0 21.29 - 28.39: 0 28.39 - 35.48: 3 Bond angle restraints: 19782 Sorted by residual: angle pdb=" N THR I 44 " pdb=" CA THR I 44 " pdb=" HA THR I 44 " ideal model delta sigma weight residual 110.00 74.52 35.48 3.00e+00 1.11e-01 1.40e+02 angle pdb=" C THR I 44 " pdb=" CA THR I 44 " pdb=" HA THR I 44 " ideal model delta sigma weight residual 109.00 74.50 34.50 3.00e+00 1.11e-01 1.32e+02 angle pdb=" CB THR I 44 " pdb=" CA THR I 44 " pdb=" HA THR I 44 " ideal model delta sigma weight residual 109.00 80.41 28.59 3.00e+00 1.11e-01 9.09e+01 angle pdb=" C LYS I 58 " pdb=" N THR I 59 " pdb=" CA THR I 59 " ideal model delta sigma weight residual 122.99 131.30 -8.31 1.41e+00 5.03e-01 3.47e+01 angle pdb=" N THR G 81 " pdb=" CA THR G 81 " pdb=" C THR G 81 " ideal model delta sigma weight residual 111.40 118.18 -6.78 1.22e+00 6.72e-01 3.09e+01 ... (remaining 19777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 4297 17.99 - 35.99: 259 35.99 - 53.98: 139 53.98 - 71.97: 268 71.97 - 89.96: 11 Dihedral angle restraints: 4974 sinusoidal: 2784 harmonic: 2190 Sorted by residual: dihedral pdb=" CA SER G 87 " pdb=" C SER G 87 " pdb=" N ILE G 88 " pdb=" CA ILE G 88 " ideal model delta harmonic sigma weight residual 180.00 149.99 30.01 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA LYS I 80 " pdb=" C LYS I 80 " pdb=" N THR I 81 " pdb=" CA THR I 81 " ideal model delta harmonic sigma weight residual -180.00 -151.46 -28.54 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA LYS L 80 " pdb=" C LYS L 80 " pdb=" N THR L 81 " pdb=" CA THR L 81 " ideal model delta harmonic sigma weight residual 180.00 -151.68 -28.32 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 4971 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 695 0.106 - 0.211: 220 0.211 - 0.316: 27 0.316 - 0.421: 5 0.421 - 0.526: 1 Chirality restraints: 948 Sorted by residual: chirality pdb=" CA THR I 44 " pdb=" N THR I 44 " pdb=" C THR I 44 " pdb=" CB THR I 44 " both_signs ideal model delta sigma weight residual False 2.53 2.00 0.53 2.00e-01 2.50e+01 6.93e+00 chirality pdb=" CA GLU H 61 " pdb=" N GLU H 61 " pdb=" C GLU H 61 " pdb=" CB GLU H 61 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CA LYS E 60 " pdb=" N LYS E 60 " pdb=" C LYS E 60 " pdb=" CB LYS E 60 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 945 not shown) Planarity restraints: 1638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN L 62 " -0.031 2.00e-02 2.50e+03 4.73e-02 3.36e+01 pdb=" CD GLN L 62 " 0.004 2.00e-02 2.50e+03 pdb=" OE1 GLN L 62 " 0.012 2.00e-02 2.50e+03 pdb=" NE2 GLN L 62 " 0.084 2.00e-02 2.50e+03 pdb="HE21 GLN L 62 " 0.004 2.00e-02 2.50e+03 pdb="HE22 GLN L 62 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN H 62 " -0.032 2.00e-02 2.50e+03 4.67e-02 3.28e+01 pdb=" CD GLN H 62 " 0.006 2.00e-02 2.50e+03 pdb=" OE1 GLN H 62 " 0.012 2.00e-02 2.50e+03 pdb=" NE2 GLN H 62 " 0.081 2.00e-02 2.50e+03 pdb="HE21 GLN H 62 " 0.005 2.00e-02 2.50e+03 pdb="HE22 GLN H 62 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN J 62 " -0.028 2.00e-02 2.50e+03 4.01e-02 2.41e+01 pdb=" CD GLN J 62 " 0.008 2.00e-02 2.50e+03 pdb=" OE1 GLN J 62 " 0.009 2.00e-02 2.50e+03 pdb=" NE2 GLN J 62 " 0.069 2.00e-02 2.50e+03 pdb="HE21 GLN J 62 " 0.004 2.00e-02 2.50e+03 pdb="HE22 GLN J 62 " -0.062 2.00e-02 2.50e+03 ... (remaining 1635 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.23: 692 2.23 - 2.80: 21431 2.80 - 3.36: 25788 3.36 - 3.93: 33978 3.93 - 4.50: 50349 Nonbonded interactions: 132238 Sorted by model distance: nonbonded pdb=" HG SER G 87 " pdb=" O SER H 87 " model vdw 1.660 2.450 nonbonded pdb=" H THR I 44 " pdb=" HA THR I 44 " model vdw 1.664 1.816 nonbonded pdb=" HG SER K 87 " pdb=" O SER L 87 " model vdw 1.683 2.450 nonbonded pdb=" HG SER I 87 " pdb=" O SER J 87 " model vdw 1.702 2.450 nonbonded pdb=" HG SER H 87 " pdb=" O SER I 87 " model vdw 1.715 2.450 ... (remaining 132233 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 37 through 91) selection = (chain 'B' and resid 37 through 91) selection = (chain 'C' and resid 37 through 91) selection = (chain 'D' and resid 37 through 91) selection = (chain 'E' and resid 37 through 91) selection = (chain 'F' and resid 37 through 91) selection = (chain 'G' and resid 37 through 91) selection = (chain 'H' and resid 37 through 91) selection = (chain 'I' and resid 37 through 91) selection = (chain 'J' and resid 37 through 91) selection = (chain 'K' and resid 37 through 91) selection = (chain 'L' and resid 37 through 91) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 0.200 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.350 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.060 ------------------------------------------------------------------------------- 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= 0.762 Angle : 1.597 8.348 7140 Z= 0.955 Chirality : 0.100 0.526 948 Planarity : 0.006 0.026 882 Dihedral : 13.679 89.965 1782 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 0.18 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.72 % Favored : 92.01 % Rotamer: Outliers : 0.76 % Allowed : 2.65 % Favored : 96.59 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.22), residues: 738 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.17), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.027 0.009 HIS A 50 PHE 0.036 0.008 PHE E 94 TYR 0.047 0.011 TYR E 39 *********************** 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 : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.4419 (t80) cc_final: 0.3934 (t80) REVERT: D 45 LYS cc_start: 0.6950 (mttt) cc_final: 0.6750 (mttt) REVERT: J 38 LEU cc_start: 0.5398 (tp) cc_final: 0.5053 (tp) REVERT: J 79 GLN cc_start: 0.4626 (OUTLIER) cc_final: 0.4104 (tp-100) outliers start: 4 outliers final: 0 residues processed: 209 average time/residue: 0.4767 time to fit residues: 121.5487 Evaluate side-chains 137 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 chunk 65 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 50 HIS ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.157795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.128201 restraints weight = 26157.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.137332 restraints weight = 12070.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.143323 restraints weight = 6604.281| |-----------------------------------------------------------------------------| r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5612 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5286 Z= 0.219 Angle : 0.652 4.379 7140 Z= 0.384 Chirality : 0.053 0.392 948 Planarity : 0.002 0.013 882 Dihedral : 7.156 22.520 768 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.23), residues: 738 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.17), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 50 PHE 0.013 0.003 PHE A 94 TYR 0.012 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.3728 (t80) cc_final: 0.3503 (t80) REVERT: B 39 TYR cc_start: 0.4014 (t80) cc_final: 0.3789 (t80) REVERT: D 88 ILE cc_start: 0.6742 (tt) cc_final: 0.6505 (pt) REVERT: G 45 LYS cc_start: 0.6781 (mmtp) cc_final: 0.6368 (mmtm) REVERT: H 45 LYS cc_start: 0.8795 (mttt) cc_final: 0.8263 (mtpt) REVERT: H 60 LYS cc_start: 0.8342 (mmtm) cc_final: 0.8123 (mmmt) REVERT: H 80 LYS cc_start: 0.8619 (ttpt) cc_final: 0.7826 (tptt) REVERT: I 60 LYS cc_start: 0.7948 (mttp) cc_final: 0.7696 (ttpt) REVERT: I 80 LYS cc_start: 0.8367 (ttpt) cc_final: 0.8142 (ptmt) REVERT: K 20 GLU cc_start: 0.7067 (mp0) cc_final: 0.6718 (mp0) REVERT: K 60 LYS cc_start: 0.7755 (ttmm) cc_final: 0.7497 (ttmm) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.5304 time to fit residues: 100.7055 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 : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 45 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 67 optimal weight: 0.0060 chunk 51 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 14 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.159955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.129094 restraints weight = 26045.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.138156 restraints weight = 12413.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.144226 restraints weight = 6932.252| |-----------------------------------------------------------------------------| r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5714 moved from start: 0.5596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5286 Z= 0.181 Angle : 0.546 4.850 7140 Z= 0.322 Chirality : 0.053 0.386 948 Planarity : 0.002 0.008 882 Dihedral : 6.202 18.794 768 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.24), residues: 738 helix: None (None), residues: 0 sheet: -0.13 (0.71), residues: 60 loop : -1.85 (0.18), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 PHE 0.019 0.002 PHE D 94 TYR 0.012 0.001 TYR L 39 *********************** 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 160 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.835 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: F 57 GLU cc_start: 0.7067 (pt0) cc_final: 0.6753 (pm20) REVERT: H 60 LYS cc_start: 0.8301 (mmtm) cc_final: 0.8045 (mmmt) REVERT: H 80 LYS cc_start: 0.8656 (ttpt) cc_final: 0.7948 (tptt) REVERT: I 60 LYS cc_start: 0.7872 (mttp) cc_final: 0.7636 (tttt) REVERT: I 80 LYS cc_start: 0.8456 (ttpt) cc_final: 0.8193 (ptmt) REVERT: J 21 LYS cc_start: 0.7428 (tmtt) cc_final: 0.7208 (tptp) REVERT: K 20 GLU cc_start: 0.6922 (mp0) cc_final: 0.6693 (mp0) REVERT: K 60 LYS cc_start: 0.7780 (ttmm) cc_final: 0.7481 (ttmm) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.5170 time to fit residues: 99.9112 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 : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 79 GLN ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.4163 r_free = 0.4163 target = 0.143096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.114157 restraints weight = 26694.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.122834 restraints weight = 12180.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.128448 restraints weight = 6644.079| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5930 moved from start: 0.6707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5286 Z= 0.331 Angle : 0.660 5.645 7140 Z= 0.384 Chirality : 0.053 0.377 948 Planarity : 0.003 0.013 882 Dihedral : 6.723 21.203 768 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.23), residues: 738 helix: None (None), residues: 0 sheet: -0.94 (0.67), residues: 60 loop : -2.31 (0.18), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS A 50 PHE 0.008 0.002 PHE E 94 TYR 0.019 0.002 TYR L 39 *********************** 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 : 0.789 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: B 42 SER cc_start: 0.7325 (t) cc_final: 0.6952 (m) REVERT: B 46 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7550 (mm-30) REVERT: C 42 SER cc_start: 0.7931 (t) cc_final: 0.7439 (m) REVERT: D 45 LYS cc_start: 0.7536 (mttt) cc_final: 0.7184 (mttt) REVERT: F 57 GLU cc_start: 0.7266 (pt0) cc_final: 0.6885 (pm20) REVERT: H 60 LYS cc_start: 0.8387 (mmtm) cc_final: 0.8118 (mmmt) REVERT: H 80 LYS cc_start: 0.8818 (ttpt) cc_final: 0.8163 (tptt) REVERT: I 60 LYS cc_start: 0.8047 (mttp) cc_final: 0.7737 (ttpt) REVERT: J 65 ASN cc_start: 0.8787 (m-40) cc_final: 0.8535 (m-40) REVERT: K 60 LYS cc_start: 0.7824 (ttmm) cc_final: 0.7546 (ttmm) REVERT: K 80 LYS cc_start: 0.8801 (ttpt) cc_final: 0.8069 (tppt) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.5295 time to fit residues: 97.5261 Evaluate side-chains 127 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 11 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** 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** ** C 79 GLN ** 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 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN ** J 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4057 r_free = 0.4057 target = 0.133629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.106983 restraints weight = 25147.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.114989 restraints weight = 11367.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.120359 restraints weight = 6140.054| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6160 moved from start: 0.7974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 5286 Z= 0.362 Angle : 0.736 7.188 7140 Z= 0.422 Chirality : 0.054 0.396 948 Planarity : 0.003 0.016 882 Dihedral : 7.309 25.334 768 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.23), residues: 738 helix: None (None), residues: 0 sheet: -1.57 (0.66), residues: 60 loop : -2.60 (0.18), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 50 PHE 0.007 0.001 PHE F 94 TYR 0.019 0.003 TYR I 39 *********************** 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 159 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 SER cc_start: 0.7253 (t) cc_final: 0.6993 (m) REVERT: B 46 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7639 (mm-30) REVERT: D 45 LYS cc_start: 0.7763 (mttt) cc_final: 0.7392 (mttt) REVERT: E 42 SER cc_start: 0.7921 (t) cc_final: 0.7718 (m) REVERT: E 57 GLU cc_start: 0.6334 (tt0) cc_final: 0.6131 (tt0) REVERT: F 57 GLU cc_start: 0.7042 (pt0) cc_final: 0.6705 (pp20) REVERT: F 88 ILE cc_start: 0.7523 (tt) cc_final: 0.7292 (pt) REVERT: H 80 LYS cc_start: 0.8734 (ttpt) cc_final: 0.8236 (tptt) REVERT: I 60 LYS cc_start: 0.8071 (mttp) cc_final: 0.7758 (ttpt) REVERT: J 65 ASN cc_start: 0.8571 (m-40) cc_final: 0.8311 (m-40) REVERT: K 20 GLU cc_start: 0.6788 (mp0) cc_final: 0.6535 (mp0) REVERT: K 80 LYS cc_start: 0.8725 (ttpt) cc_final: 0.7965 (tppt) REVERT: L 80 LYS cc_start: 0.7497 (tptp) cc_final: 0.6905 (tppt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.5104 time to fit residues: 98.0784 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 : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 14 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 2 optimal weight: 0.0770 chunk 7 optimal weight: 2.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- 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** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 GLN ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4159 r_free = 0.4159 target = 0.137344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.110245 restraints weight = 25010.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.118028 restraints weight = 11353.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.123229 restraints weight = 6191.292| |-----------------------------------------------------------------------------| r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6158 moved from start: 0.8339 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= 0.228 Angle : 0.585 4.992 7140 Z= 0.340 Chirality : 0.052 0.384 948 Planarity : 0.002 0.010 882 Dihedral : 6.599 24.793 768 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.24), residues: 738 helix: None (None), residues: 0 sheet: -1.41 (0.70), residues: 60 loop : -2.45 (0.19), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 50 PHE 0.009 0.002 PHE B 94 TYR 0.013 0.002 TYR I 39 *********************** 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 : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7473 (mm-30) REVERT: D 45 LYS cc_start: 0.7624 (mttt) cc_final: 0.7299 (mttt) REVERT: D 60 LYS cc_start: 0.8332 (tttp) cc_final: 0.8008 (tmtt) REVERT: D 61 GLU cc_start: 0.6638 (tp30) cc_final: 0.6359 (tp30) REVERT: E 45 LYS cc_start: 0.8095 (tptm) cc_final: 0.7832 (mtpp) REVERT: F 57 GLU cc_start: 0.6914 (pt0) cc_final: 0.6678 (pp20) REVERT: I 60 LYS cc_start: 0.8044 (mttp) cc_final: 0.7754 (ttpt) REVERT: J 21 LYS cc_start: 0.7829 (tmtt) cc_final: 0.7534 (tptp) REVERT: J 65 ASN cc_start: 0.8448 (m-40) cc_final: 0.8112 (m-40) REVERT: K 80 LYS cc_start: 0.8649 (ttpt) cc_final: 0.7899 (tppt) REVERT: L 80 LYS cc_start: 0.7453 (tptp) cc_final: 0.6854 (tppt) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.5282 time to fit residues: 104.8981 Evaluate side-chains 140 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 31 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4081 r_free = 0.4081 target = 0.129826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.103532 restraints weight = 25810.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.110975 restraints weight = 11576.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.115997 restraints weight = 6255.550| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.9311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 5286 Z= 0.410 Angle : 0.768 5.657 7140 Z= 0.447 Chirality : 0.055 0.412 948 Planarity : 0.004 0.014 882 Dihedral : 7.735 24.442 768 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 22.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.79 % Favored : 88.21 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.23), residues: 738 helix: None (None), residues: 0 sheet: -2.54 (0.63), residues: 60 loop : -2.79 (0.18), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS A 50 PHE 0.008 0.002 PHE F 94 TYR 0.021 0.003 TYR I 39 *********************** 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 : 0.793 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 46 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7325 (mm-30) REVERT: D 45 LYS cc_start: 0.7770 (mttt) cc_final: 0.7370 (mttt) REVERT: D 60 LYS cc_start: 0.8233 (tttp) cc_final: 0.7907 (tmtt) REVERT: E 45 LYS cc_start: 0.8247 (tptm) cc_final: 0.7999 (mtpp) REVERT: H 80 LYS cc_start: 0.8748 (ttpt) cc_final: 0.8312 (tptt) REVERT: I 60 LYS cc_start: 0.8009 (mttp) cc_final: 0.7775 (ttpt) REVERT: K 80 LYS cc_start: 0.8670 (ttpt) cc_final: 0.8023 (tppt) REVERT: L 83 GLU cc_start: 0.7824 (tp30) cc_final: 0.7618 (tp30) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.5092 time to fit residues: 96.0897 Evaluate side-chains 128 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 61 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 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 = 0.4086 r_free = 0.4086 target = 0.131248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.104206 restraints weight = 26690.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.111828 restraints weight = 12095.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.117035 restraints weight = 6618.580| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 moved from start: 0.9563 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= 0.271 Angle : 0.633 6.090 7140 Z= 0.367 Chirality : 0.052 0.394 948 Planarity : 0.003 0.011 882 Dihedral : 7.056 23.815 768 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.33 % Favored : 87.67 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.24), residues: 738 helix: None (None), residues: 0 sheet: -2.23 (0.68), residues: 60 loop : -2.66 (0.19), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 50 PHE 0.006 0.001 PHE F 94 TYR 0.013 0.002 TYR L 39 *********************** 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 159 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.818 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: A 80 LYS cc_start: 0.6664 (mmpt) cc_final: 0.6366 (mmmm) REVERT: B 46 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7423 (mm-30) REVERT: D 45 LYS cc_start: 0.7746 (mttt) cc_final: 0.7355 (mttt) REVERT: D 60 LYS cc_start: 0.8363 (tttp) cc_final: 0.7995 (tmtt) REVERT: D 79 GLN cc_start: 0.6718 (tp-100) cc_final: 0.6453 (tp-100) REVERT: E 45 LYS cc_start: 0.8207 (tptm) cc_final: 0.7902 (mtpp) REVERT: E 46 GLU cc_start: 0.7515 (tp30) cc_final: 0.7287 (mm-30) REVERT: E 60 LYS cc_start: 0.7200 (mttt) cc_final: 0.6945 (mmtm) REVERT: E 79 GLN cc_start: 0.7678 (tt0) cc_final: 0.7278 (tp-100) REVERT: F 57 GLU cc_start: 0.7185 (pt0) cc_final: 0.6927 (pm20) REVERT: H 80 LYS cc_start: 0.8793 (ttpt) cc_final: 0.8319 (tptt) REVERT: I 60 LYS cc_start: 0.8121 (mttp) cc_final: 0.7812 (ttpt) REVERT: I 65 ASN cc_start: 0.8681 (m-40) cc_final: 0.8481 (m-40) REVERT: J 21 LYS cc_start: 0.7904 (tmtt) cc_final: 0.7655 (tptp) REVERT: K 80 LYS cc_start: 0.8734 (ttpt) cc_final: 0.8062 (tppt) REVERT: L 83 GLU cc_start: 0.7655 (tp30) cc_final: 0.7443 (tp30) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.5038 time to fit residues: 97.3972 Evaluate side-chains 142 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 62 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 E 65 ASN F 65 ASN G 65 ASN J 65 ASN ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.135141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.108561 restraints weight = 24911.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.116195 restraints weight = 11324.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.121367 restraints weight = 6115.670| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6249 moved from start: 0.9770 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= 0.182 Angle : 0.541 4.522 7140 Z= 0.314 Chirality : 0.053 0.388 948 Planarity : 0.002 0.012 882 Dihedral : 6.364 22.469 768 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.38 % Favored : 88.62 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.25), residues: 738 helix: None (None), residues: 0 sheet: -2.00 (0.67), residues: 60 loop : -2.43 (0.19), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 50 PHE 0.008 0.002 PHE C 94 TYR 0.012 0.002 TYR E 39 *********************** 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 165 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.793 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 61 GLU cc_start: 0.6607 (tm-30) cc_final: 0.5893 (tm-30) REVERT: B 46 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7575 (mm-30) REVERT: C 97 LYS cc_start: 0.8521 (mmtm) cc_final: 0.8313 (mmtm) REVERT: D 45 LYS cc_start: 0.7813 (mttt) cc_final: 0.7423 (mttt) REVERT: D 60 LYS cc_start: 0.8336 (tttp) cc_final: 0.7880 (tmtt) REVERT: D 61 GLU cc_start: 0.6603 (tp30) cc_final: 0.6299 (tp30) REVERT: E 45 LYS cc_start: 0.8130 (tptm) cc_final: 0.7841 (mtpp) REVERT: E 46 GLU cc_start: 0.7524 (tp30) cc_final: 0.7159 (mm-30) REVERT: E 60 LYS cc_start: 0.7180 (mttt) cc_final: 0.6850 (mmtm) REVERT: H 80 LYS cc_start: 0.8647 (ttpt) cc_final: 0.8240 (tptt) REVERT: I 60 LYS cc_start: 0.8073 (mttp) cc_final: 0.7733 (tmmt) REVERT: K 80 LYS cc_start: 0.8639 (ttpt) cc_final: 0.7967 (tppt) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.4882 time to fit residues: 98.0380 Evaluate side-chains 142 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 21 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** K 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 = 0.4044 r_free = 0.4044 target = 0.132127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.105342 restraints weight = 25855.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.113349 restraints weight = 11883.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.118708 restraints weight = 6441.661| |-----------------------------------------------------------------------------| r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6204 moved from start: 0.9867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5286 Z= 0.181 Angle : 0.539 4.546 7140 Z= 0.312 Chirality : 0.053 0.384 948 Planarity : 0.002 0.012 882 Dihedral : 6.094 21.533 768 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.25), residues: 738 helix: None (None), residues: 0 sheet: -1.98 (0.65), residues: 60 loop : -2.33 (0.20), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 50 PHE 0.007 0.002 PHE B 94 TYR 0.012 0.002 TYR E 39 ********************** 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 164 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.6568 (tm-30) cc_final: 0.5763 (tm-30) REVERT: B 46 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7627 (mm-30) REVERT: C 97 LYS cc_start: 0.8512 (mmtm) cc_final: 0.8287 (mmtm) REVERT: D 45 LYS cc_start: 0.7836 (mttt) cc_final: 0.7470 (mttt) REVERT: D 60 LYS cc_start: 0.8278 (tttp) cc_final: 0.7880 (tmtt) REVERT: D 61 GLU cc_start: 0.6563 (tp30) cc_final: 0.6259 (tp30) REVERT: D 79 GLN cc_start: 0.7281 (tt0) cc_final: 0.7071 (tt0) REVERT: E 45 LYS cc_start: 0.8286 (tptm) cc_final: 0.7849 (mtpp) REVERT: E 46 GLU cc_start: 0.7604 (tp30) cc_final: 0.7246 (tp30) REVERT: E 60 LYS cc_start: 0.7215 (mttt) cc_final: 0.6841 (mmtm) REVERT: H 80 LYS cc_start: 0.8733 (ttpt) cc_final: 0.8296 (tptt) REVERT: I 60 LYS cc_start: 0.8099 (mttp) cc_final: 0.7755 (ttpt) REVERT: K 20 GLU cc_start: 0.6747 (mp0) cc_final: 0.6333 (mp0) REVERT: K 80 LYS cc_start: 0.8684 (ttpt) cc_final: 0.7987 (tppt) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.4891 time to fit residues: 97.8115 Evaluate side-chains 143 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 44 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 59 optimal weight: 0.0070 chunk 23 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN ** 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** ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4033 r_free = 0.4033 target = 0.131467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.105083 restraints weight = 26167.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.113010 restraints weight = 12047.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.118246 restraints weight = 6540.826| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6227 moved from start: 1.0131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5286 Z= 0.198 Angle : 0.535 4.455 7140 Z= 0.311 Chirality : 0.052 0.385 948 Planarity : 0.002 0.010 882 Dihedral : 6.043 21.218 768 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.92 % Favored : 88.08 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.25), residues: 738 helix: None (None), residues: 0 sheet: -2.04 (0.67), residues: 60 loop : -2.33 (0.20), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.007 0.001 PHE B 94 TYR 0.010 0.002 TYR E 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4770.73 seconds wall clock time: 84 minutes 55.00 seconds (5095.00 seconds total)