Starting phenix.real_space_refine on Sat Aug 23 17:02:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g6v_29785/08_2025/8g6v_29785.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g6v_29785/08_2025/8g6v_29785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g6v_29785/08_2025/8g6v_29785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g6v_29785/08_2025/8g6v_29785.map" model { file = "/net/cci-nas-00/data/ceres_data/8g6v_29785/08_2025/8g6v_29785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g6v_29785/08_2025/8g6v_29785.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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 S 72 5.16 5 C 8932 2.51 5 N 2248 2.21 5 O 2484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13736 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1136 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 11, 'TRANS': 130} Chain: "A" Number of atoms: 1155 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 143, 1144 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Conformer: "B" Number of residues, atoms: 143, 1144 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} bond proxies already assigned to first conformer: 1167 Chain: "C" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1151 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 12, 'TRANS': 131} Chain: "D" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1144 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "E" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1151 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 12, 'TRANS': 131} Chain: "G" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1144 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "F" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1144 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "H" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1151 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 12, 'TRANS': 131} Chain: "I" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1129 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 11, 'TRANS': 129} Chain: "K" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1136 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 11, 'TRANS': 130} Chain: "J" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1144 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "L" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1151 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 12, 'TRANS': 131} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 112 " occ=0.12 ... (20 atoms not shown) pdb=" NH2BARG A 112 " occ=0.88 Time building chain proxies: 3.03, per 1000 atoms: 0.22 Number of scatterers: 13736 At special positions: 0 Unit cell: (178.08, 181.44, 72.8, 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) S 72 16.00 O 2484 8.00 N 2248 7.00 C 8932 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS D 61 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS G 61 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS H 61 " distance=2.04 Simple disulfide: pdb=" SG CYS I 61 " - pdb=" SG CYS K 61 " distance=2.03 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS L 61 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 455.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3290 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 0 sheets defined 74.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'B' and resid 26 through 38 removed outlier: 3.754A pdb=" N ASP B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 44 Processing helix chain 'B' and resid 49 through 75 removed outlier: 3.746A pdb=" N THR B 53 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 54 " --> pdb=" O PRO B 50 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 55 " --> pdb=" O HIS B 51 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN B 57 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 111 removed outlier: 4.654A pdb=" N MET B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLY B 94 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 95 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS B 96 " --> pdb=" O ASN B 92 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE B 97 " --> pdb=" O MET B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 128 removed outlier: 3.591A pdb=" N VAL B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR B 128 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 17 Processing helix chain 'A' and resid 26 through 38 Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 49 through 76 removed outlier: 3.595A pdb=" N GLN A 57 " --> pdb=" O THR A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 110 removed outlier: 5.678A pdb=" N GLY A 94 " --> pdb=" O ASN A 90 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LEU A 95 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE A 97 " --> pdb=" O MET A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 128 removed outlier: 3.600A pdb=" N VAL A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A 128 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 17 Processing helix chain 'C' and resid 18 through 19 No H-bonds generated for 'chain 'C' and resid 18 through 19' Processing helix chain 'C' and resid 20 through 24 removed outlier: 3.931A pdb=" N PHE C 24 " --> pdb=" O SER C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 39 removed outlier: 3.623A pdb=" N LEU C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 44 removed outlier: 3.775A pdb=" N SER C 44 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 75 removed outlier: 3.812A pdb=" N THR C 53 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA C 54 " --> pdb=" O PRO C 50 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU C 55 " --> pdb=" O HIS C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 111 removed outlier: 4.729A pdb=" N GLY C 94 " --> pdb=" O ASN C 90 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU C 95 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS C 96 " --> pdb=" O ASN C 92 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE C 97 " --> pdb=" O MET C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 128 Processing helix chain 'D' and resid 12 through 17 Processing helix chain 'D' and resid 26 through 43 removed outlier: 3.813A pdb=" N ARG D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N GLU D 40 " --> pdb=" O ALA D 36 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 76 removed outlier: 3.743A pdb=" N THR D 53 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA D 54 " --> pdb=" O PRO D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 93 Processing helix chain 'D' and resid 94 through 111 Processing helix chain 'D' and resid 111 through 128 removed outlier: 3.775A pdb=" N VAL D 120 " --> pdb=" O ILE D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 133 removed outlier: 3.563A pdb=" N ARG D 133 " --> pdb=" O PRO D 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 17 Processing helix chain 'E' and resid 18 through 19 No H-bonds generated for 'chain 'E' and resid 18 through 19' Processing helix chain 'E' and resid 20 through 24 removed outlier: 4.071A pdb=" N PHE E 24 " --> pdb=" O SER E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 39 removed outlier: 3.507A pdb=" N LEU E 37 " --> pdb=" O THR E 33 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG E 39 " --> pdb=" O SER E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 75 Processing helix chain 'E' and resid 78 through 93 removed outlier: 3.710A pdb=" N VAL E 86 " --> pdb=" O ARG E 82 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 111 removed outlier: 3.903A pdb=" N PHE E 97 " --> pdb=" O MET E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 128 Processing helix chain 'G' and resid 12 through 17 Processing helix chain 'G' and resid 26 through 43 removed outlier: 3.787A pdb=" N ARG G 39 " --> pdb=" O SER G 35 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N GLU G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ALA G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 76 Processing helix chain 'G' and resid 78 through 111 removed outlier: 3.547A pdb=" N ARG G 82 " --> pdb=" O ASP G 78 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLY G 94 " --> pdb=" O ASN G 90 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS G 96 " --> pdb=" O ASN G 92 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE G 97 " --> pdb=" O MET G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 128 removed outlier: 3.743A pdb=" N GLU G 117 " --> pdb=" O GLU G 113 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL G 120 " --> pdb=" O ILE G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 133 removed outlier: 3.533A pdb=" N ARG G 133 " --> pdb=" O PRO G 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 17 Processing helix chain 'F' and resid 26 through 43 removed outlier: 3.788A pdb=" N ARG F 39 " --> pdb=" O SER F 35 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLU F 40 " --> pdb=" O ALA F 36 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.753A pdb=" N THR F 53 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA F 54 " --> pdb=" O PRO F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 111 removed outlier: 4.663A pdb=" N GLY F 94 " --> pdb=" O ASN F 90 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LYS F 96 " --> pdb=" O ASN F 92 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE F 97 " --> pdb=" O MET F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 128 removed outlier: 3.868A pdb=" N VAL F 120 " --> pdb=" O ILE F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 133 removed outlier: 3.564A pdb=" N ARG F 133 " --> pdb=" O PRO F 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 17 Processing helix chain 'H' and resid 18 through 19 No H-bonds generated for 'chain 'H' and resid 18 through 19' Processing helix chain 'H' and resid 20 through 24 removed outlier: 3.689A pdb=" N PHE H 24 " --> pdb=" O SER H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 38 removed outlier: 3.570A pdb=" N LEU H 30 " --> pdb=" O SER H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 43 Processing helix chain 'H' and resid 49 through 75 removed outlier: 3.505A pdb=" N GLN H 57 " --> pdb=" O THR H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 93 Processing helix chain 'H' and resid 93 through 111 removed outlier: 4.131A pdb=" N PHE H 97 " --> pdb=" O MET H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 128 removed outlier: 3.660A pdb=" N THR H 128 " --> pdb=" O VAL H 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 10 Processing helix chain 'I' and resid 12 through 17 Processing helix chain 'I' and resid 26 through 38 Processing helix chain 'I' and resid 38 through 44 Processing helix chain 'I' and resid 49 through 76 removed outlier: 3.969A pdb=" N THR I 53 " --> pdb=" O SER I 49 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA I 54 " --> pdb=" O PRO I 50 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU I 55 " --> pdb=" O HIS I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 111 removed outlier: 3.553A pdb=" N LEU I 84 " --> pdb=" O ALA I 80 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N MET I 93 " --> pdb=" O VAL I 89 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLY I 94 " --> pdb=" O ASN I 90 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU I 95 " --> pdb=" O THR I 91 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS I 96 " --> pdb=" O ASN I 92 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE I 97 " --> pdb=" O MET I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 127 Processing helix chain 'K' and resid 12 through 17 Processing helix chain 'K' and resid 26 through 38 Processing helix chain 'K' and resid 38 through 43 Processing helix chain 'K' and resid 49 through 76 removed outlier: 3.571A pdb=" N GLN K 57 " --> pdb=" O THR K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 110 removed outlier: 3.629A pdb=" N ASP K 83 " --> pdb=" O PRO K 79 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU K 84 " --> pdb=" O ALA K 80 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N GLY K 94 " --> pdb=" O ASN K 90 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU K 95 " --> pdb=" O THR K 91 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS K 96 " --> pdb=" O ASN K 92 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE K 97 " --> pdb=" O MET K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 128 removed outlier: 3.707A pdb=" N THR K 128 " --> pdb=" O VAL K 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 12 through 17 Processing helix chain 'J' and resid 26 through 43 removed outlier: 4.011A pdb=" N ASP J 32 " --> pdb=" O ARG J 28 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG J 39 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N GLU J 40 " --> pdb=" O ALA J 36 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA J 41 " --> pdb=" O LEU J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 76 removed outlier: 3.749A pdb=" N THR J 53 " --> pdb=" O SER J 49 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA J 54 " --> pdb=" O PRO J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 110 removed outlier: 3.732A pdb=" N VAL J 86 " --> pdb=" O ARG J 82 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLY J 94 " --> pdb=" O ASN J 90 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS J 96 " --> pdb=" O ASN J 92 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE J 97 " --> pdb=" O MET J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 128 removed outlier: 3.574A pdb=" N ARG J 127 " --> pdb=" O GLY J 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 12 through 17 Processing helix chain 'L' and resid 26 through 36 Processing helix chain 'L' and resid 49 through 75 removed outlier: 3.530A pdb=" N GLN L 57 " --> pdb=" O THR L 53 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU L 65 " --> pdb=" O CYS L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 93 Processing helix chain 'L' and resid 93 through 111 removed outlier: 3.699A pdb=" N PHE L 97 " --> pdb=" O MET L 93 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU L 108 " --> pdb=" O HIS L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 128 removed outlier: 3.615A pdb=" N THR L 128 " --> pdb=" O VAL L 124 " (cutoff:3.500A) 869 hydrogen bonds defined for protein. 2580 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: 1.72 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4325 1.34 - 1.47: 3605 1.47 - 1.59: 6122 1.59 - 1.72: 1 1.72 - 1.85: 108 Bond restraints: 14161 Sorted by residual: bond pdb=" CB PRO L 144 " pdb=" CG PRO L 144 " ideal model delta sigma weight residual 1.492 1.610 -0.118 5.00e-02 4.00e+02 5.55e+00 bond pdb=" CG PRO E 144 " pdb=" CD PRO E 144 " ideal model delta sigma weight residual 1.503 1.574 -0.071 3.40e-02 8.65e+02 4.30e+00 bond pdb=" CB PRO E 144 " pdb=" CG PRO E 144 " ideal model delta sigma weight residual 1.492 1.576 -0.084 5.00e-02 4.00e+02 2.82e+00 bond pdb=" CB PRO E 79 " pdb=" CG PRO E 79 " ideal model delta sigma weight residual 1.492 1.570 -0.078 5.00e-02 4.00e+02 2.42e+00 bond pdb=" CG PRO L 144 " pdb=" CD PRO L 144 " ideal model delta sigma weight residual 1.503 1.555 -0.052 3.40e-02 8.65e+02 2.30e+00 ... (remaining 14156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 19321 3.20 - 6.40: 59 6.40 - 9.60: 6 9.60 - 12.80: 2 12.80 - 16.00: 2 Bond angle restraints: 19390 Sorted by residual: angle pdb=" CA PRO L 144 " pdb=" N PRO L 144 " pdb=" CD PRO L 144 " ideal model delta sigma weight residual 112.00 104.87 7.13 1.40e+00 5.10e-01 2.59e+01 angle pdb=" CA LEU J 84 " pdb=" CB LEU J 84 " pdb=" CG LEU J 84 " ideal model delta sigma weight residual 116.30 132.30 -16.00 3.50e+00 8.16e-02 2.09e+01 angle pdb=" CA PRO E 79 " pdb=" N PRO E 79 " pdb=" CD PRO E 79 " ideal model delta sigma weight residual 112.00 105.75 6.25 1.40e+00 5.10e-01 1.99e+01 angle pdb=" CA LEU G 84 " pdb=" CB LEU G 84 " pdb=" CG LEU G 84 " ideal model delta sigma weight residual 116.30 130.33 -14.03 3.50e+00 8.16e-02 1.61e+01 angle pdb=" CA PRO E 144 " pdb=" N PRO E 144 " pdb=" CD PRO E 144 " ideal model delta sigma weight residual 112.00 106.97 5.03 1.40e+00 5.10e-01 1.29e+01 ... (remaining 19385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 7114 17.50 - 35.00: 962 35.00 - 52.50: 250 52.50 - 70.00: 22 70.00 - 87.50: 9 Dihedral angle restraints: 8357 sinusoidal: 3301 harmonic: 5056 Sorted by residual: dihedral pdb=" CB CYS C 61 " pdb=" SG CYS C 61 " pdb=" SG CYS D 61 " pdb=" CB CYS D 61 " ideal model delta sinusoidal sigma weight residual -86.00 -154.12 68.12 1 1.00e+01 1.00e-02 6.02e+01 dihedral pdb=" CA ASN J 90 " pdb=" C ASN J 90 " pdb=" N THR J 91 " pdb=" CA THR J 91 " ideal model delta harmonic sigma weight residual 180.00 144.79 35.21 0 5.00e+00 4.00e-02 4.96e+01 dihedral pdb=" CA ASN K 90 " pdb=" C ASN K 90 " pdb=" N THR K 91 " pdb=" CA THR K 91 " ideal model delta harmonic sigma weight residual 180.00 154.64 25.36 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 8354 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1434 0.031 - 0.062: 545 0.062 - 0.092: 147 0.092 - 0.123: 62 0.123 - 0.154: 5 Chirality restraints: 2193 Sorted by residual: chirality pdb=" CB VAL H 86 " pdb=" CA VAL H 86 " pdb=" CG1 VAL H 86 " pdb=" CG2 VAL H 86 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA ASN G 90 " pdb=" N ASN G 90 " pdb=" C ASN G 90 " pdb=" CB ASN G 90 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA ASN A 90 " pdb=" N ASN A 90 " pdb=" C ASN A 90 " pdb=" CB ASN A 90 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.12e-01 ... (remaining 2190 not shown) Planarity restraints: 2455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 78 " -0.093 5.00e-02 4.00e+02 1.38e-01 3.04e+01 pdb=" N PRO E 79 " 0.238 5.00e-02 4.00e+02 pdb=" CA PRO E 79 " -0.074 5.00e-02 4.00e+02 pdb=" CD PRO E 79 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 78 " -0.050 5.00e-02 4.00e+02 7.55e-02 9.11e+00 pdb=" N PRO C 79 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO C 79 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 79 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 89 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.50e+00 pdb=" C VAL H 89 " 0.032 2.00e-02 2.50e+03 pdb=" O VAL H 89 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN H 90 " -0.011 2.00e-02 2.50e+03 ... (remaining 2452 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 131 2.65 - 3.21: 12290 3.21 - 3.77: 21390 3.77 - 4.34: 27868 4.34 - 4.90: 47630 Nonbonded interactions: 109309 Sorted by model distance: nonbonded pdb=" OG SER K 26 " pdb=" OD1 ASP K 29 " model vdw 2.084 3.040 nonbonded pdb=" OG SER A 26 " pdb=" OD1 ASP A 29 " model vdw 2.148 3.040 nonbonded pdb=" OD2 ASP G 78 " pdb=" OG SER G 81 " model vdw 2.224 3.040 nonbonded pdb=" OD2 ASP F 78 " pdb=" OG SER F 81 " model vdw 2.276 3.040 nonbonded pdb=" OD2 ASP D 78 " pdb=" OG SER D 81 " model vdw 2.304 3.040 ... (remaining 109304 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 111 or resid 113 through 141)) selection = (chain 'B' and (resid 1 through 111 or resid 113 through 141)) selection = (chain 'C' and (resid 1 through 111 or resid 113 through 141)) selection = (chain 'D' and (resid 1 through 111 or resid 113 through 141)) selection = (chain 'E' and (resid 1 through 111 or resid 113 through 141)) selection = (chain 'F' and (resid 1 through 111 or resid 113 through 141)) selection = (chain 'G' and (resid 1 through 111 or resid 113 through 141)) selection = (chain 'H' and (resid 1 through 111 or resid 113 through 141)) selection = (chain 'I' and (resid 1 through 111 or resid 113 through 141)) selection = (chain 'J' and (resid 1 through 111 or resid 113 through 141)) selection = (chain 'K' and (resid 1 through 111 or resid 113 through 141)) selection = (chain 'L' and (resid 1 through 111 or resid 113 through 141)) } 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=0.12 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 7.400 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: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.300 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 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 : 0.003 0.118 14166 Z= 0.128 Angle : 0.600 15.996 19400 Z= 0.314 Chirality : 0.037 0.154 2193 Planarity : 0.006 0.138 2455 Dihedral : 16.349 87.499 5052 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.85 % Allowed : 24.72 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.21), residues: 1695 helix: 1.40 (0.15), residues: 1221 sheet: None (None), residues: 0 loop : 0.40 (0.31), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 82 TYR 0.013 0.001 TYR J 132 PHE 0.009 0.001 PHE F 122 TRP 0.024 0.001 TRP F 71 HIS 0.007 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00299 (14161) covalent geometry : angle 0.59556 (19390) SS BOND : bond 0.00366 ( 5) SS BOND : angle 3.13160 ( 10) hydrogen bonds : bond 0.10480 ( 869) hydrogen bonds : angle 4.35946 ( 2580) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 373 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASN cc_start: 0.8616 (t0) cc_final: 0.8205 (t0) REVERT: G 82 ARG cc_start: 0.7999 (ttp-110) cc_final: 0.7637 (mtp85) REVERT: F 64 GLU cc_start: 0.7802 (tp30) cc_final: 0.7407 (tp30) REVERT: F 91 THR cc_start: 0.8407 (m) cc_final: 0.8205 (p) REVERT: H 93 MET cc_start: 0.7758 (mmt) cc_final: 0.6627 (mmt) REVERT: I 78 ASP cc_start: 0.7274 (t70) cc_final: 0.6996 (t70) REVERT: K 75 ASN cc_start: 0.8385 (t0) cc_final: 0.8173 (t0) REVERT: L 127 ARG cc_start: 0.6821 (tpt170) cc_final: 0.4822 (tmt-80) outliers start: 12 outliers final: 5 residues processed: 376 average time/residue: 0.1024 time to fit residues: 55.6397 Evaluate side-chains 369 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 364 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain H residue 66 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 HIS A 47 HIS D 90 ASN F 90 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.093347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.071310 restraints weight = 29064.978| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 1.98 r_work: 0.2565 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2429 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2398 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2398 r_free = 0.2398 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2398 r_free = 0.2398 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2398 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14166 Z= 0.186 Angle : 0.584 10.409 19400 Z= 0.293 Chirality : 0.041 0.149 2193 Planarity : 0.006 0.081 2455 Dihedral : 4.445 44.293 1875 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.15 % Allowed : 23.28 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.21), residues: 1695 helix: 1.62 (0.15), residues: 1222 sheet: None (None), residues: 0 loop : 0.19 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 82 TYR 0.009 0.001 TYR I 118 PHE 0.016 0.001 PHE K 97 TRP 0.013 0.001 TRP F 71 HIS 0.008 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00454 (14161) covalent geometry : angle 0.58059 (19390) SS BOND : bond 0.00793 ( 5) SS BOND : angle 2.76335 ( 10) hydrogen bonds : bond 0.05242 ( 869) hydrogen bonds : angle 4.54816 ( 2580) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 366 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8541 (tpp-160) cc_final: 0.8182 (tpm170) REVERT: B 61 CYS cc_start: 0.8588 (m) cc_final: 0.8114 (t) REVERT: D 82 ARG cc_start: 0.8273 (mtm-85) cc_final: 0.8009 (mtm110) REVERT: E 64 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7459 (mm-30) REVERT: F 18 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8332 (t80) REVERT: F 64 GLU cc_start: 0.8305 (tp30) cc_final: 0.7802 (mt-10) REVERT: F 91 THR cc_start: 0.8543 (m) cc_final: 0.8320 (p) REVERT: F 112 ARG cc_start: 0.8231 (ttm170) cc_final: 0.8004 (ttp-110) REVERT: K 75 ASN cc_start: 0.8463 (t0) cc_final: 0.8234 (t0) REVERT: J 82 ARG cc_start: 0.7690 (mtm-85) cc_final: 0.7437 (mtm-85) outliers start: 47 outliers final: 33 residues processed: 388 average time/residue: 0.0995 time to fit residues: 55.5088 Evaluate side-chains 388 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 354 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain F residue 7 LYS Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 66 MET Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 139 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 45 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 chunk 144 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 ASN F 90 ASN J 90 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.092532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.068942 restraints weight = 40011.759| |-----------------------------------------------------------------------------| r_work (start): 0.2601 rms_B_bonded: 2.41 r_work: 0.2450 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2450 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2472 r_free = 0.2472 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2472 r_free = 0.2472 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14166 Z= 0.187 Angle : 0.572 9.870 19400 Z= 0.289 Chirality : 0.041 0.151 2193 Planarity : 0.006 0.065 2455 Dihedral : 4.078 33.829 1863 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.52 % Allowed : 21.97 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.21), residues: 1695 helix: 1.64 (0.15), residues: 1223 sheet: None (None), residues: 0 loop : 0.05 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 82 TYR 0.008 0.001 TYR K 88 PHE 0.018 0.001 PHE K 97 TRP 0.015 0.001 TRP F 71 HIS 0.006 0.001 HIS E 47 Details of bonding type rmsd covalent geometry : bond 0.00460 (14161) covalent geometry : angle 0.56893 (19390) SS BOND : bond 0.00442 ( 5) SS BOND : angle 2.68265 ( 10) hydrogen bonds : bond 0.05423 ( 869) hydrogen bonds : angle 4.60612 ( 2580) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 363 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.6901 (mtm) REVERT: B 28 ARG cc_start: 0.8463 (tpp-160) cc_final: 0.8097 (tpm170) REVERT: B 32 ASP cc_start: 0.8488 (m-30) cc_final: 0.8286 (m-30) REVERT: B 61 CYS cc_start: 0.8405 (m) cc_final: 0.7958 (t) REVERT: D 18 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8328 (t80) REVERT: G 82 ARG cc_start: 0.8172 (mtm-85) cc_final: 0.7853 (mtp85) REVERT: F 18 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8462 (t80) REVERT: F 64 GLU cc_start: 0.8104 (tp30) cc_final: 0.7630 (mt-10) REVERT: F 91 THR cc_start: 0.8515 (m) cc_final: 0.8270 (p) REVERT: H 76 LEU cc_start: 0.6178 (OUTLIER) cc_final: 0.5971 (tt) REVERT: K 75 ASN cc_start: 0.8529 (t0) cc_final: 0.8282 (t0) outliers start: 68 outliers final: 46 residues processed: 399 average time/residue: 0.1018 time to fit residues: 58.9062 Evaluate side-chains 404 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 354 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 107 CYS Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 107 CYS Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 139 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 136 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 1 optimal weight: 0.0770 chunk 133 optimal weight: 7.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 ASN G 99 GLN F 90 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.095027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.072030 restraints weight = 37731.103| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 2.45 r_work: 0.2522 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2516 r_free = 0.2516 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2516 r_free = 0.2516 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2516 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14166 Z= 0.108 Angle : 0.510 11.353 19400 Z= 0.255 Chirality : 0.037 0.146 2193 Planarity : 0.005 0.054 2455 Dihedral : 3.869 34.077 1863 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.00 % Allowed : 22.62 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.21), residues: 1695 helix: 1.87 (0.15), residues: 1218 sheet: None (None), residues: 0 loop : 0.34 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 127 TYR 0.007 0.001 TYR K 88 PHE 0.014 0.001 PHE K 97 TRP 0.013 0.001 TRP F 71 HIS 0.003 0.001 HIS G 104 Details of bonding type rmsd covalent geometry : bond 0.00233 (14161) covalent geometry : angle 0.50733 (19390) SS BOND : bond 0.00526 ( 5) SS BOND : angle 2.35673 ( 10) hydrogen bonds : bond 0.04075 ( 869) hydrogen bonds : angle 4.45857 ( 2580) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 370 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8418 (tpp-160) cc_final: 0.7913 (tpm170) REVERT: B 32 ASP cc_start: 0.8548 (m-30) cc_final: 0.8306 (m-30) REVERT: B 61 CYS cc_start: 0.8399 (m) cc_final: 0.7968 (t) REVERT: C 76 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6806 (mp) REVERT: D 18 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.8449 (t80) REVERT: E 29 ASP cc_start: 0.9033 (m-30) cc_final: 0.8695 (m-30) REVERT: F 18 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8475 (t80) REVERT: F 61 CYS cc_start: 0.7482 (t) cc_final: 0.7015 (t) REVERT: F 64 GLU cc_start: 0.7989 (tp30) cc_final: 0.7573 (mt-10) REVERT: F 96 LYS cc_start: 0.8832 (ptpt) cc_final: 0.8571 (ptmt) REVERT: H 61 CYS cc_start: 0.7757 (t) cc_final: 0.7551 (t) REVERT: K 75 ASN cc_start: 0.8490 (t0) cc_final: 0.8258 (t0) outliers start: 60 outliers final: 34 residues processed: 403 average time/residue: 0.1051 time to fit residues: 61.3093 Evaluate side-chains 393 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 356 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 107 CYS Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 160 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 161 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 55 optimal weight: 0.0770 chunk 157 optimal weight: 4.9990 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 ASN K 47 HIS K 99 GLN J 90 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.091931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.068490 restraints weight = 39002.917| |-----------------------------------------------------------------------------| r_work (start): 0.2594 rms_B_bonded: 2.36 r_work: 0.2444 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2305 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2312 r_free = 0.2312 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2312 r_free = 0.2312 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2312 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14166 Z= 0.204 Angle : 0.595 10.533 19400 Z= 0.299 Chirality : 0.042 0.160 2193 Planarity : 0.006 0.052 2455 Dihedral : 4.067 33.597 1863 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.52 % Allowed : 22.36 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.21), residues: 1695 helix: 1.74 (0.15), residues: 1224 sheet: None (None), residues: 0 loop : 0.07 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 127 TYR 0.010 0.001 TYR K 88 PHE 0.019 0.001 PHE K 97 TRP 0.017 0.001 TRP F 71 HIS 0.008 0.002 HIS E 47 Details of bonding type rmsd covalent geometry : bond 0.00508 (14161) covalent geometry : angle 0.59160 (19390) SS BOND : bond 0.00764 ( 5) SS BOND : angle 2.85072 ( 10) hydrogen bonds : bond 0.05524 ( 869) hydrogen bonds : angle 4.63913 ( 2580) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 359 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8600 (tpp-160) cc_final: 0.8361 (tpm170) REVERT: B 61 CYS cc_start: 0.8596 (m) cc_final: 0.8155 (t) REVERT: C 16 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9298 (tp) REVERT: C 76 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6745 (mp) REVERT: D 18 PHE cc_start: 0.9151 (OUTLIER) cc_final: 0.8421 (t80) REVERT: E 29 ASP cc_start: 0.9140 (m-30) cc_final: 0.8840 (m-30) REVERT: F 18 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8494 (t80) REVERT: F 61 CYS cc_start: 0.8592 (t) cc_final: 0.8231 (t) REVERT: F 64 GLU cc_start: 0.8346 (tp30) cc_final: 0.7712 (mt-10) REVERT: F 96 LYS cc_start: 0.8993 (ptpt) cc_final: 0.8779 (ptmt) REVERT: I 14 GLU cc_start: 0.9012 (mp0) cc_final: 0.8520 (mp0) REVERT: K 75 ASN cc_start: 0.8519 (t0) cc_final: 0.8281 (t0) REVERT: J 133 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8340 (ptp-170) outliers start: 68 outliers final: 53 residues processed: 399 average time/residue: 0.0996 time to fit residues: 58.0475 Evaluate side-chains 406 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 348 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 96 LYS Chi-restraints excluded: chain G residue 107 CYS Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 107 CYS Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 6 TYR Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 139 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 49 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 164 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 163 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.092987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.068918 restraints weight = 48329.118| |-----------------------------------------------------------------------------| r_work (start): 0.2589 rms_B_bonded: 2.81 r_work: 0.2421 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2421 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2428 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2428 r_free = 0.2428 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2428 r_free = 0.2428 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2428 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 14166 Z= 0.187 Angle : 0.579 10.917 19400 Z= 0.291 Chirality : 0.041 0.158 2193 Planarity : 0.005 0.048 2455 Dihedral : 4.087 32.464 1863 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.66 % Allowed : 22.62 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.21), residues: 1695 helix: 1.71 (0.15), residues: 1219 sheet: None (None), residues: 0 loop : 0.02 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 39 TYR 0.009 0.001 TYR K 88 PHE 0.017 0.001 PHE K 97 TRP 0.017 0.001 TRP F 71 HIS 0.007 0.001 HIS E 47 Details of bonding type rmsd covalent geometry : bond 0.00461 (14161) covalent geometry : angle 0.57373 (19390) SS BOND : bond 0.00462 ( 5) SS BOND : angle 3.32507 ( 10) hydrogen bonds : bond 0.05326 ( 869) hydrogen bonds : angle 4.63622 ( 2580) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 354 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 CYS cc_start: 0.8411 (m) cc_final: 0.8075 (t) REVERT: C 76 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6646 (mp) REVERT: D 18 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8391 (t80) REVERT: E 29 ASP cc_start: 0.9065 (m-30) cc_final: 0.8768 (m-30) REVERT: F 18 PHE cc_start: 0.9159 (OUTLIER) cc_final: 0.8473 (t80) REVERT: F 64 GLU cc_start: 0.8202 (tp30) cc_final: 0.7642 (mt-10) REVERT: F 96 LYS cc_start: 0.8933 (ptpt) cc_final: 0.8694 (ptmt) REVERT: H 16 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9289 (tp) REVERT: H 107 CYS cc_start: 0.9309 (OUTLIER) cc_final: 0.8939 (m) REVERT: I 14 GLU cc_start: 0.8802 (mp0) cc_final: 0.8258 (mp0) REVERT: K 75 ASN cc_start: 0.8493 (t0) cc_final: 0.8241 (t0) REVERT: J 133 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8087 (ptp90) outliers start: 70 outliers final: 50 residues processed: 397 average time/residue: 0.0949 time to fit residues: 54.8526 Evaluate side-chains 408 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 352 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 22 ASP Chi-restraints excluded: chain D residue 107 CYS Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 107 CYS Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 107 CYS Chi-restraints excluded: chain L residue 139 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 34 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 133 optimal weight: 20.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 ASN K 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.094916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.072069 restraints weight = 46203.567| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 2.65 r_work: 0.2504 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2522 r_free = 0.2522 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2522 r_free = 0.2522 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14166 Z= 0.106 Angle : 0.524 11.006 19400 Z= 0.263 Chirality : 0.037 0.157 2193 Planarity : 0.005 0.045 2455 Dihedral : 3.864 35.022 1863 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.08 % Allowed : 23.87 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.21 (0.21), residues: 1695 helix: 1.91 (0.15), residues: 1214 sheet: None (None), residues: 0 loop : 0.44 (0.30), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 127 TYR 0.007 0.001 TYR K 88 PHE 0.011 0.001 PHE K 97 TRP 0.018 0.001 TRP F 71 HIS 0.003 0.001 HIS E 47 Details of bonding type rmsd covalent geometry : bond 0.00231 (14161) covalent geometry : angle 0.51877 (19390) SS BOND : bond 0.00458 ( 5) SS BOND : angle 3.41671 ( 10) hydrogen bonds : bond 0.03801 ( 869) hydrogen bonds : angle 4.46120 ( 2580) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 351 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 ASP cc_start: 0.8651 (m-30) cc_final: 0.8350 (m-30) REVERT: B 61 CYS cc_start: 0.8484 (m) cc_final: 0.8047 (t) REVERT: C 76 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6710 (mp) REVERT: D 18 PHE cc_start: 0.9088 (OUTLIER) cc_final: 0.8435 (t80) REVERT: E 29 ASP cc_start: 0.9022 (m-30) cc_final: 0.8713 (m-30) REVERT: E 64 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7254 (mm-30) REVERT: G 22 ASP cc_start: 0.8665 (p0) cc_final: 0.8245 (p0) REVERT: F 18 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.8586 (t80) REVERT: F 64 GLU cc_start: 0.8142 (tp30) cc_final: 0.7590 (mt-10) REVERT: I 14 GLU cc_start: 0.8780 (mp0) cc_final: 0.8319 (mp0) REVERT: K 75 ASN cc_start: 0.8441 (t0) cc_final: 0.8220 (t0) REVERT: L 29 ASP cc_start: 0.9109 (m-30) cc_final: 0.8774 (m-30) outliers start: 46 outliers final: 30 residues processed: 380 average time/residue: 0.0979 time to fit residues: 54.3837 Evaluate side-chains 375 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 342 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 107 CYS Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain K residue 6 TYR Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 139 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 129 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 154 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.093309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.070117 restraints weight = 39430.664| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 2.32 r_work: 0.2546 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2514 r_free = 0.2514 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2514 r_free = 0.2514 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14166 Z= 0.123 Angle : 0.552 10.796 19400 Z= 0.278 Chirality : 0.038 0.157 2193 Planarity : 0.005 0.044 2455 Dihedral : 3.863 35.357 1863 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.95 % Allowed : 24.13 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.21), residues: 1695 helix: 1.97 (0.15), residues: 1212 sheet: None (None), residues: 0 loop : 0.47 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 82 TYR 0.006 0.001 TYR J 132 PHE 0.014 0.001 PHE K 97 TRP 0.020 0.001 TRP F 71 HIS 0.004 0.001 HIS E 47 Details of bonding type rmsd covalent geometry : bond 0.00287 (14161) covalent geometry : angle 0.54248 (19390) SS BOND : bond 0.00345 ( 5) SS BOND : angle 4.53683 ( 10) hydrogen bonds : bond 0.04019 ( 869) hydrogen bonds : angle 4.50775 ( 2580) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 349 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 ASP cc_start: 0.8639 (m-30) cc_final: 0.8331 (m-30) REVERT: B 61 CYS cc_start: 0.8396 (m) cc_final: 0.8001 (t) REVERT: C 76 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.6647 (mp) REVERT: D 16 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8622 (mp) REVERT: D 18 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8432 (t80) REVERT: E 29 ASP cc_start: 0.8964 (m-30) cc_final: 0.8681 (m-30) REVERT: G 22 ASP cc_start: 0.8579 (p0) cc_final: 0.8178 (p0) REVERT: F 18 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.8578 (t80) REVERT: F 64 GLU cc_start: 0.8105 (tp30) cc_final: 0.7619 (mt-10) REVERT: F 90 ASN cc_start: 0.8460 (p0) cc_final: 0.8199 (p0) REVERT: F 96 LYS cc_start: 0.8840 (ptpt) cc_final: 0.8632 (ptmt) REVERT: I 14 GLU cc_start: 0.8690 (mp0) cc_final: 0.8222 (mp0) REVERT: K 75 ASN cc_start: 0.8470 (t0) cc_final: 0.8248 (t0) REVERT: J 133 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7677 (ptp90) REVERT: L 29 ASP cc_start: 0.9050 (m-30) cc_final: 0.8760 (m-30) outliers start: 44 outliers final: 35 residues processed: 378 average time/residue: 0.0928 time to fit residues: 51.0774 Evaluate side-chains 383 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 343 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 107 CYS Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 107 CYS Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 107 CYS Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain K residue 6 TYR Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 139 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 31 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 114 optimal weight: 0.0570 chunk 96 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 overall best weight: 1.9304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.095294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.073072 restraints weight = 42952.344| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 2.54 r_work: 0.2482 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2529 r_free = 0.2529 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2529 r_free = 0.2529 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14166 Z= 0.125 Angle : 0.557 11.037 19400 Z= 0.281 Chirality : 0.038 0.159 2193 Planarity : 0.005 0.044 2455 Dihedral : 3.839 33.049 1863 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.67 % Allowed : 23.61 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.37 (0.21), residues: 1695 helix: 2.10 (0.15), residues: 1186 sheet: None (None), residues: 0 loop : 0.41 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 82 TYR 0.006 0.001 TYR K 88 PHE 0.014 0.001 PHE K 97 TRP 0.022 0.001 TRP F 71 HIS 0.004 0.001 HIS E 47 Details of bonding type rmsd covalent geometry : bond 0.00292 (14161) covalent geometry : angle 0.54570 (19390) SS BOND : bond 0.00363 ( 5) SS BOND : angle 5.02736 ( 10) hydrogen bonds : bond 0.04056 ( 869) hydrogen bonds : angle 4.51194 ( 2580) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 352 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 ASP cc_start: 0.8717 (m-30) cc_final: 0.8399 (m-30) REVERT: B 61 CYS cc_start: 0.8465 (m) cc_final: 0.8049 (t) REVERT: C 76 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6619 (mp) REVERT: D 16 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8584 (mp) REVERT: D 18 PHE cc_start: 0.9090 (OUTLIER) cc_final: 0.8548 (t80) REVERT: E 29 ASP cc_start: 0.8973 (m-30) cc_final: 0.8712 (m-30) REVERT: G 22 ASP cc_start: 0.8678 (p0) cc_final: 0.8255 (p0) REVERT: F 16 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8597 (mp) REVERT: F 18 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8593 (t80) REVERT: F 64 GLU cc_start: 0.8189 (tp30) cc_final: 0.7661 (mt-10) REVERT: I 14 GLU cc_start: 0.8764 (mp0) cc_final: 0.8282 (mp0) REVERT: K 75 ASN cc_start: 0.8464 (t0) cc_final: 0.8205 (t0) REVERT: J 133 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7746 (ptp90) REVERT: L 29 ASP cc_start: 0.9055 (m-30) cc_final: 0.8807 (m-30) outliers start: 55 outliers final: 44 residues processed: 387 average time/residue: 0.0944 time to fit residues: 53.2877 Evaluate side-chains 400 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 350 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 107 CYS Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 107 CYS Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 107 CYS Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 90 ASN Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 139 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 105 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 47 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.093126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.069661 restraints weight = 38391.700| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 2.37 r_work: 0.2508 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2538 r_free = 0.2538 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2538 r_free = 0.2538 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14166 Z= 0.143 Angle : 0.582 10.924 19400 Z= 0.294 Chirality : 0.039 0.158 2193 Planarity : 0.005 0.043 2455 Dihedral : 3.862 33.365 1863 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.41 % Allowed : 23.67 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.21), residues: 1695 helix: 2.08 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : 0.38 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 82 TYR 0.007 0.001 TYR J 132 PHE 0.015 0.001 PHE K 97 TRP 0.022 0.001 TRP F 71 HIS 0.004 0.001 HIS J 104 Details of bonding type rmsd covalent geometry : bond 0.00344 (14161) covalent geometry : angle 0.56533 (19390) SS BOND : bond 0.00438 ( 5) SS BOND : angle 6.09781 ( 10) hydrogen bonds : bond 0.04230 ( 869) hydrogen bonds : angle 4.54327 ( 2580) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 351 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 ASP cc_start: 0.8662 (m-30) cc_final: 0.8361 (m-30) REVERT: B 61 CYS cc_start: 0.8369 (m) cc_final: 0.8069 (t) REVERT: C 76 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6579 (mp) REVERT: D 16 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8567 (mp) REVERT: D 18 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.8538 (t80) REVERT: E 29 ASP cc_start: 0.8951 (m-30) cc_final: 0.8691 (m-30) REVERT: G 71 TRP cc_start: 0.8432 (t60) cc_final: 0.8100 (t60) REVERT: F 16 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8656 (mp) REVERT: F 18 PHE cc_start: 0.9120 (OUTLIER) cc_final: 0.8578 (t80) REVERT: F 64 GLU cc_start: 0.8127 (tp30) cc_final: 0.7606 (mt-10) REVERT: F 90 ASN cc_start: 0.8395 (p0) cc_final: 0.8162 (p0) REVERT: I 14 GLU cc_start: 0.8735 (mp0) cc_final: 0.8205 (mp0) REVERT: K 75 ASN cc_start: 0.8426 (t0) cc_final: 0.8150 (t0) REVERT: J 32 ASP cc_start: 0.8643 (m-30) cc_final: 0.8438 (m-30) REVERT: J 71 TRP cc_start: 0.8463 (t60) cc_final: 0.8218 (t60) REVERT: J 133 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.7723 (ptp90) REVERT: L 29 ASP cc_start: 0.9006 (m-30) cc_final: 0.8753 (m-30) outliers start: 51 outliers final: 42 residues processed: 383 average time/residue: 0.0989 time to fit residues: 55.0706 Evaluate side-chains 399 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 351 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 107 CYS Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 107 CYS Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 107 CYS Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 139 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 47 optimal weight: 1.9990 chunk 160 optimal weight: 7.9990 chunk 155 optimal weight: 0.0470 chunk 41 optimal weight: 0.1980 chunk 38 optimal weight: 5.9990 chunk 133 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 122 optimal weight: 0.0040 chunk 134 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 overall best weight: 1.4494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.095293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.072313 restraints weight = 37334.268| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 2.29 r_work: 0.2538 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2403 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2454 r_free = 0.2454 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2454 r_free = 0.2454 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14166 Z= 0.119 Angle : 0.561 10.891 19400 Z= 0.283 Chirality : 0.038 0.160 2193 Planarity : 0.005 0.043 2455 Dihedral : 3.811 33.735 1863 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.15 % Allowed : 24.13 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.41 (0.21), residues: 1695 helix: 2.12 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : 0.46 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 82 TYR 0.009 0.001 TYR I 88 PHE 0.013 0.001 PHE K 97 TRP 0.023 0.001 TRP F 71 HIS 0.004 0.001 HIS J 104 Details of bonding type rmsd covalent geometry : bond 0.00271 (14161) covalent geometry : angle 0.55068 (19390) SS BOND : bond 0.00616 ( 5) SS BOND : angle 4.68826 ( 10) hydrogen bonds : bond 0.03918 ( 869) hydrogen bonds : angle 4.50019 ( 2580) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3077.77 seconds wall clock time: 53 minutes 14.52 seconds (3194.52 seconds total)