Starting phenix.real_space_refine on Fri Mar 15 06:17:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ncj_12268/03_2024/7ncj_12268.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ncj_12268/03_2024/7ncj_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ncj_12268/03_2024/7ncj_12268.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ncj_12268/03_2024/7ncj_12268.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ncj_12268/03_2024/7ncj_12268.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ncj_12268/03_2024/7ncj_12268.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.15, per 1000 atoms: 0.47 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 - 3.50 Amino acid : False - 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: 8.30 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.97 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: 3.59 Time building geometry restraints manager: 8.63 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: 74.50 - 85.86: 3 85.86 - 97.22: 0 97.22 - 108.58: 4795 108.58 - 119.94: 11703 119.94 - 131.30: 3281 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 1.850 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 1.850 nonbonded pdb=" HG SER I 87 " pdb=" O SER J 87 " model vdw 1.702 1.850 nonbonded pdb=" HG SER H 87 " pdb=" O SER I 87 " model vdw 1.715 1.850 ... (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 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: 0.690 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: 0.180 Extract box with map and model: 3.880 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 37.250 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.730 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 4 poor density : 205 time to evaluate : 0.807 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: 0.4675 time to fit residues: 119.3662 Evaluate side-chains 137 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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: 0.9990 chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 0.1980 chunk 18 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5310 moved from start: 0.4572 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= 0.199 Angle : 0.644 4.481 7140 Z= 0.378 Chirality : 0.053 0.386 948 Planarity : 0.002 0.011 882 Dihedral : 7.109 22.654 768 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % 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 (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: -2.63 (0.22), residues: 738 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.17), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 PHE 0.013 0.003 PHE D 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 155 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 88 ILE cc_start: 0.6064 (tt) cc_final: 0.5850 (pt) REVERT: F 44 THR cc_start: 0.7554 (p) cc_final: 0.7271 (p) REVERT: G 45 LYS cc_start: 0.6082 (mmtp) cc_final: 0.5649 (mmtm) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.5212 time to fit residues: 96.7091 Evaluate side-chains 133 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS C 50 HIS E 50 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5458 moved from start: 0.5845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5286 Z= 0.188 Angle : 0.563 4.215 7140 Z= 0.331 Chirality : 0.053 0.381 948 Planarity : 0.002 0.008 882 Dihedral : 6.293 19.809 768 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.24), residues: 738 helix: None (None), residues: 0 sheet: -0.41 (0.70), residues: 60 loop : -1.99 (0.18), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.007 0.001 PHE B 94 TYR 0.016 0.002 TYR C 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 154 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.820 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: D 88 ILE cc_start: 0.6243 (tt) cc_final: 0.6009 (pt) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.5165 time to fit residues: 96.8449 Evaluate side-chains 128 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5679 moved from start: 0.6925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5286 Z= 0.263 Angle : 0.610 6.767 7140 Z= 0.353 Chirality : 0.052 0.381 948 Planarity : 0.003 0.013 882 Dihedral : 6.364 20.305 768 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % 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: -2.77 (0.24), residues: 738 helix: None (None), residues: 0 sheet: -0.68 (0.71), residues: 60 loop : -2.20 (0.18), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 50 PHE 0.004 0.001 PHE A 94 TYR 0.016 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 154 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.649 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 outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.4844 time to fit residues: 90.3728 Evaluate side-chains 127 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5861 moved from start: 0.7906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 5286 Z= 0.373 Angle : 0.689 4.592 7140 Z= 0.401 Chirality : 0.053 0.371 948 Planarity : 0.003 0.015 882 Dihedral : 7.004 23.539 768 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Rotamer: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % 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 (0.23), residues: 738 helix: None (None), residues: 0 sheet: -1.27 (0.69), residues: 60 loop : -2.52 (0.18), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 50 PHE 0.009 0.002 PHE E 94 TYR 0.019 0.003 TYR B 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 149 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 ILE cc_start: 0.6281 (tt) cc_final: 0.5955 (tt) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.5190 time to fit residues: 93.2382 Evaluate side-chains 127 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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** ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5826 moved from start: 0.8329 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= 0.224 Angle : 0.570 5.021 7140 Z= 0.331 Chirality : 0.052 0.381 948 Planarity : 0.002 0.018 882 Dihedral : 6.311 23.120 768 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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: -3.07 (0.24), residues: 738 helix: None (None), residues: 0 sheet: -1.19 (0.73), residues: 60 loop : -2.39 (0.18), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 50 PHE 0.006 0.001 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 158 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.754 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 outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.5083 time to fit residues: 96.4989 Evaluate side-chains 133 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 41 optimal weight: 0.0020 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN C 79 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5832 moved from start: 0.8680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5286 Z= 0.189 Angle : 0.537 5.704 7140 Z= 0.313 Chirality : 0.053 0.383 948 Planarity : 0.002 0.008 882 Dihedral : 5.993 22.434 768 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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: -2.92 (0.25), residues: 738 helix: None (None), residues: 0 sheet: -1.06 (0.75), residues: 60 loop : -2.28 (0.19), 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 0.011 0.002 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 fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 74 VAL cc_start: 0.5739 (t) cc_final: 0.5489 (t) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.5239 time to fit residues: 97.9616 Evaluate side-chains 132 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 overall best weight: 1.1188 ------------------------------------------------------------------------------- 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** ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5874 moved from start: 0.9005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5286 Z= 0.223 Angle : 0.566 6.395 7140 Z= 0.326 Chirality : 0.053 0.383 948 Planarity : 0.002 0.013 882 Dihedral : 6.010 22.475 768 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.79 % Favored : 88.21 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % 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 (0.25), residues: 738 helix: None (None), residues: 0 sheet: -1.23 (0.72), residues: 60 loop : -2.28 (0.19), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 50 PHE 0.005 0.001 PHE B 94 TYR 0.014 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 156 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 0.878 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: K 20 GLU cc_start: 0.6128 (mp0) cc_final: 0.5400 (mp0) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.5165 time to fit residues: 96.9734 Evaluate side-chains 133 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 0.0570 chunk 64 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5839 moved from start: 0.9141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5286 Z= 0.174 Angle : 0.508 4.462 7140 Z= 0.294 Chirality : 0.053 0.385 948 Planarity : 0.002 0.009 882 Dihedral : 5.706 21.607 768 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.26), residues: 738 helix: None (None), residues: 0 sheet: -1.12 (0.73), residues: 60 loop : -2.14 (0.20), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 50 PHE 0.007 0.001 PHE B 94 TYR 0.010 0.001 TYR L 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 157 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.762 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: E 79 GLN cc_start: 0.6865 (tt0) cc_final: 0.6298 (tp40) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.5070 time to fit residues: 95.5748 Evaluate side-chains 135 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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** ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6056 moved from start: 0.9862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 5286 Z= 0.378 Angle : 0.704 5.157 7140 Z= 0.409 Chirality : 0.054 0.386 948 Planarity : 0.003 0.017 882 Dihedral : 7.017 22.701 768 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 26.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % 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: -3.35 (0.24), residues: 738 helix: None (None), residues: 0 sheet: -2.26 (0.62), residues: 60 loop : -2.50 (0.19), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS H 50 PHE 0.008 0.002 PHE F 94 TYR 0.019 0.003 TYR G 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 150 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 0.803 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 outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.5209 time to fit residues: 94.1837 Evaluate side-chains 126 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 3 optimal weight: 0.1980 chunk 41 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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** ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN 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 = 0.4232 r_free = 0.4232 target = 0.139349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.113257 restraints weight = 23768.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.120719 restraints weight = 10790.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.125688 restraints weight = 5817.642| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6227 moved from start: 0.9939 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= 0.186 Angle : 0.547 4.689 7140 Z= 0.314 Chirality : 0.053 0.387 948 Planarity : 0.002 0.014 882 Dihedral : 6.131 22.275 768 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.84 % Favored : 89.16 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.25), residues: 738 helix: None (None), residues: 0 sheet: -1.94 (0.64), residues: 60 loop : -2.33 (0.19), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 50 PHE 0.010 0.001 PHE B 94 TYR 0.011 0.002 TYR C 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3810.84 seconds wall clock time: 67 minutes 16.06 seconds (4036.06 seconds total)