Starting phenix.real_space_refine on Thu May 15 19:11:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g6v_29785/05_2025/8g6v_29785.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g6v_29785/05_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_29785/05_2025/8g6v_29785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g6v_29785/05_2025/8g6v_29785.map" model { file = "/net/cci-nas-00/data/ceres_data/8g6v_29785/05_2025/8g6v_29785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g6v_29785/05_2025/8g6v_29785.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.33, per 1000 atoms: 0.68 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: 3.44 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.14 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: 3.80 Time building geometry restraints manager: 4.01 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: 3.630 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: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.850 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.970 ------------------------------------------------------------------------------- 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 : 5.69 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.024 0.001 TRP F 71 HIS 0.007 0.001 HIS B 47 PHE 0.009 0.001 PHE F 122 TYR 0.013 0.001 TYR J 132 ARG 0.010 0.000 ARG J 82 Details of bonding type rmsd hydrogen bonds : bond 0.10480 ( 869) hydrogen bonds : angle 4.35946 ( 2580) SS BOND : bond 0.00366 ( 5) SS BOND : angle 3.13160 ( 10) covalent geometry : bond 0.00299 (14161) covalent geometry : angle 0.59556 (19390) *********************** 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 : 1.432 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: 0.6995 (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: 0.4823 (tmt-80) outliers start: 12 outliers final: 5 residues processed: 376 average time/residue: 0.2462 time to fit residues: 132.2271 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 : 1.494 ------------------------------------------------------------------------------- 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 141 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 70 optimal weight: 0.0570 chunk 43 optimal weight: 7.9990 chunk 85 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 131 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 152 optimal weight: 0.5980 overall best weight: 1.4902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 HIS D 90 ASN F 90 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.095546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.072483 restraints weight = 40910.004| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 2.39 r_work: 0.2557 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.0790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14166 Z= 0.115 Angle : 0.524 10.885 19400 Z= 0.260 Chirality : 0.037 0.136 2193 Planarity : 0.005 0.079 2455 Dihedral : 4.287 44.877 1875 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.43 % Allowed : 23.54 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.21), residues: 1695 helix: 1.72 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : 0.44 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 71 HIS 0.005 0.001 HIS B 47 PHE 0.014 0.001 PHE K 97 TYR 0.009 0.001 TYR I 88 ARG 0.006 0.000 ARG J 82 Details of bonding type rmsd hydrogen bonds : bond 0.04209 ( 869) hydrogen bonds : angle 4.37262 ( 2580) SS BOND : bond 0.00395 ( 5) SS BOND : angle 2.69193 ( 10) covalent geometry : bond 0.00260 (14161) covalent geometry : angle 0.52011 (19390) *********************** 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 404 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 368 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8463 (tpp-160) cc_final: 0.8133 (tpm170) REVERT: D 82 ARG cc_start: 0.8245 (mtm-85) cc_final: 0.8004 (mtm110) REVERT: E 29 ASP cc_start: 0.8999 (m-30) cc_final: 0.8622 (m-30) REVERT: G 82 ARG cc_start: 0.8082 (ttp-110) cc_final: 0.7635 (mtp85) REVERT: F 18 PHE cc_start: 0.9140 (OUTLIER) cc_final: 0.8456 (t80) REVERT: F 64 GLU cc_start: 0.8016 (tp30) cc_final: 0.7717 (mt-10) REVERT: F 96 LYS cc_start: 0.8859 (ptpt) cc_final: 0.8506 (ptmt) REVERT: I 78 ASP cc_start: 0.7382 (t70) cc_final: 0.7092 (t70) REVERT: K 75 ASN cc_start: 0.8377 (t0) cc_final: 0.8169 (t0) outliers start: 36 outliers final: 16 residues processed: 383 average time/residue: 0.2498 time to fit residues: 137.1983 Evaluate side-chains 374 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 357 time to evaluate : 1.569 ------------------------------------------------------------------------------- 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 96 LYS 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 F residue 18 PHE 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 K residue 70 THR Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 133 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 158 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 121 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS D 90 ASN F 90 ASN J 90 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.095614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.072653 restraints weight = 42657.343| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 2.61 r_work: 0.2543 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2519 r_free = 0.2519 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2519 r_free = 0.2519 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.0956 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= 0.109 Angle : 0.502 11.304 19400 Z= 0.249 Chirality : 0.037 0.142 2193 Planarity : 0.005 0.062 2455 Dihedral : 3.739 35.006 1863 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.95 % Allowed : 22.75 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.21), residues: 1695 helix: 1.85 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : 0.53 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 71 HIS 0.003 0.001 HIS J 104 PHE 0.015 0.001 PHE K 97 TYR 0.007 0.001 TYR K 88 ARG 0.003 0.000 ARG H 127 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 869) hydrogen bonds : angle 4.36456 ( 2580) SS BOND : bond 0.00298 ( 5) SS BOND : angle 2.11493 ( 10) covalent geometry : bond 0.00247 (14161) covalent geometry : angle 0.49992 (19390) *********************** 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 404 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 360 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8491 (tpp-160) cc_final: 0.8110 (tpm170) REVERT: G 77 GLU cc_start: 0.6002 (pm20) cc_final: 0.5726 (pm20) REVERT: G 82 ARG cc_start: 0.8071 (ttp-110) cc_final: 0.7667 (mtp85) REVERT: F 18 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8469 (t80) REVERT: F 64 GLU cc_start: 0.8035 (tp30) cc_final: 0.7604 (mt-10) REVERT: F 96 LYS cc_start: 0.8846 (ptpt) cc_final: 0.8494 (ptmt) REVERT: K 75 ASN cc_start: 0.8399 (t0) cc_final: 0.8178 (t0) outliers start: 44 outliers final: 27 residues processed: 384 average time/residue: 0.2491 time to fit residues: 137.3367 Evaluate side-chains 376 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 348 time to evaluate : 1.508 ------------------------------------------------------------------------------- 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 96 LYS 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 A residue 26 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain D residue 16 LEU 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 G residue 16 LEU Chi-restraints excluded: chain G residue 27 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 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 89 VAL Chi-restraints excluded: chain I residue 113 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 L residue 74 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 chunk 70 optimal weight: 0.0170 chunk 34 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 154 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 overall best weight: 2.2024 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.094377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.071314 restraints weight = 37758.355| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 2.32 r_work: 0.2526 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2391 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2432 r_free = 0.2432 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2432 r_free = 0.2432 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14166 Z= 0.124 Angle : 0.510 11.472 19400 Z= 0.254 Chirality : 0.038 0.147 2193 Planarity : 0.005 0.054 2455 Dihedral : 3.726 33.621 1863 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.54 % Allowed : 22.36 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.21), residues: 1695 helix: 1.92 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : 0.52 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 71 HIS 0.004 0.001 HIS J 104 PHE 0.015 0.001 PHE K 97 TYR 0.006 0.001 TYR I 118 ARG 0.003 0.000 ARG H 127 Details of bonding type rmsd hydrogen bonds : bond 0.04144 ( 869) hydrogen bonds : angle 4.39588 ( 2580) SS BOND : bond 0.00439 ( 5) SS BOND : angle 2.45192 ( 10) covalent geometry : bond 0.00292 (14161) covalent geometry : angle 0.50751 (19390) *********************** 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 415 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 362 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8588 (tpp-160) cc_final: 0.8185 (tpm170) REVERT: B 61 CYS cc_start: 0.8610 (m) cc_final: 0.8101 (t) REVERT: E 29 ASP cc_start: 0.9140 (m-30) cc_final: 0.8858 (m-30) REVERT: G 77 GLU cc_start: 0.6452 (pm20) cc_final: 0.6212 (pm20) REVERT: G 82 ARG cc_start: 0.8136 (ttp-110) cc_final: 0.7621 (mtp85) REVERT: F 18 PHE cc_start: 0.9182 (OUTLIER) cc_final: 0.8506 (t80) REVERT: F 64 GLU cc_start: 0.8194 (tp30) cc_final: 0.7700 (mt-10) REVERT: F 96 LYS cc_start: 0.8952 (ptpt) cc_final: 0.8599 (ptmt) REVERT: K 75 ASN cc_start: 0.8491 (t0) cc_final: 0.8280 (t0) REVERT: L 29 ASP cc_start: 0.9192 (m-30) cc_final: 0.8907 (m-30) REVERT: L 77 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7341 (pm20) REVERT: L 91 THR cc_start: 0.8776 (m) cc_final: 0.8539 (m) outliers start: 53 outliers final: 39 residues processed: 391 average time/residue: 0.2424 time to fit residues: 136.4258 Evaluate side-chains 395 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 354 time to evaluate : 1.443 ------------------------------------------------------------------------------- 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 96 LYS Chi-restraints excluded: chain B residue 113 GLU 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 66 MET Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 82 ARG 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 16 LEU Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 27 VAL 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 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 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 66 MET Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 GLU Chi-restraints excluded: chain L residue 139 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 130 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 68 optimal weight: 0.5980 chunk 89 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 chunk 125 optimal weight: 0.0270 overall best weight: 2.9244 ------------------------------------------------------------------------------- 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 K 47 HIS J 90 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.094094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.071821 restraints weight = 42230.433| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 2.49 r_work: 0.2465 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2494 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2494 r_free = 0.2494 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2494 r_free = 0.2494 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2494 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14166 Z= 0.145 Angle : 0.527 11.123 19400 Z= 0.265 Chirality : 0.039 0.156 2193 Planarity : 0.005 0.051 2455 Dihedral : 3.813 34.568 1863 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.80 % Allowed : 22.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.21), residues: 1695 helix: 1.94 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : 0.42 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 71 HIS 0.005 0.001 HIS E 47 PHE 0.016 0.001 PHE K 97 TYR 0.007 0.001 TYR I 118 ARG 0.004 0.000 ARG H 127 Details of bonding type rmsd hydrogen bonds : bond 0.04569 ( 869) hydrogen bonds : angle 4.46555 ( 2580) SS BOND : bond 0.00537 ( 5) SS BOND : angle 2.23353 ( 10) covalent geometry : bond 0.00349 (14161) covalent geometry : angle 0.52431 (19390) *********************** 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 422 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 365 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8532 (tpp-160) cc_final: 0.8159 (tpm170) REVERT: B 61 CYS cc_start: 0.8481 (m) cc_final: 0.8042 (t) REVERT: C 76 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6784 (mp) REVERT: D 18 PHE cc_start: 0.9086 (OUTLIER) cc_final: 0.8450 (t80) REVERT: E 29 ASP cc_start: 0.9052 (m-30) cc_final: 0.8750 (m-30) REVERT: G 82 ARG cc_start: 0.8165 (ttp-110) cc_final: 0.7651 (mtp85) REVERT: F 18 PHE cc_start: 0.9156 (OUTLIER) cc_final: 0.8489 (t80) REVERT: F 64 GLU cc_start: 0.8032 (tp30) cc_final: 0.7565 (mt-10) REVERT: F 96 LYS cc_start: 0.8935 (ptpt) cc_final: 0.8535 (ptmt) REVERT: K 75 ASN cc_start: 0.8476 (t0) cc_final: 0.8250 (t0) REVERT: L 77 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7331 (pm20) outliers start: 57 outliers final: 45 residues processed: 397 average time/residue: 0.2509 time to fit residues: 143.7433 Evaluate side-chains 405 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 356 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 117 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 70 THR Chi-restraints excluded: chain A residue 76 LEU 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 66 MET Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 82 ARG 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 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 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 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 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 66 MET Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 GLU 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 57 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 chunk 134 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 148 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 = 0.3101 r_free = 0.3101 target = 0.093741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.071137 restraints weight = 41730.097| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 2.44 r_work: 0.2494 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2532 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2532 r_free = 0.2532 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2532 r_free = 0.2532 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2532 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14166 Z= 0.141 Angle : 0.534 11.124 19400 Z= 0.268 Chirality : 0.039 0.161 2193 Planarity : 0.005 0.048 2455 Dihedral : 3.835 33.259 1863 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.21), residues: 1695 helix: 1.96 (0.15), residues: 1218 sheet: None (None), residues: 0 loop : 0.43 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 71 HIS 0.004 0.001 HIS E 47 PHE 0.015 0.001 PHE K 97 TYR 0.007 0.001 TYR I 118 ARG 0.005 0.000 ARG F 82 Details of bonding type rmsd hydrogen bonds : bond 0.04505 ( 869) hydrogen bonds : angle 4.47885 ( 2580) SS BOND : bond 0.00384 ( 5) SS BOND : angle 2.76818 ( 10) covalent geometry : bond 0.00338 (14161) covalent geometry : angle 0.53044 (19390) *********************** 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 421 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 361 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8471 (tpp-160) cc_final: 0.8102 (tpm170) REVERT: B 61 CYS cc_start: 0.8447 (m) cc_final: 0.8036 (t) REVERT: C 76 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6734 (mp) REVERT: D 18 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.8459 (t80) REVERT: E 29 ASP cc_start: 0.9014 (m-30) cc_final: 0.8731 (m-30) REVERT: G 77 GLU cc_start: 0.6153 (pm20) cc_final: 0.5948 (pm20) REVERT: G 82 ARG cc_start: 0.8155 (ttp-110) cc_final: 0.7661 (mtp85) REVERT: F 18 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.8488 (t80) REVERT: F 64 GLU cc_start: 0.7978 (tp30) cc_final: 0.7534 (mt-10) REVERT: F 96 LYS cc_start: 0.8875 (ptpt) cc_final: 0.8496 (ptmt) REVERT: K 75 ASN cc_start: 0.8481 (t0) cc_final: 0.8252 (t0) REVERT: L 29 ASP cc_start: 0.9075 (m-30) cc_final: 0.8752 (m-30) REVERT: L 77 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7382 (pm20) outliers start: 60 outliers final: 49 residues processed: 395 average time/residue: 0.2730 time to fit residues: 156.9822 Evaluate side-chains 410 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 357 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 96 LYS 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 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 A residue 76 LEU Chi-restraints excluded: chain C residue 66 MET 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 66 MET Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 82 ARG 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 65 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 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 L residue 74 VAL Chi-restraints excluded: chain L residue 77 GLU 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 18 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 4 optimal weight: 0.2980 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 155 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 163 optimal weight: 5.9990 chunk 111 optimal weight: 0.0370 overall best weight: 0.9660 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.096305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.073761 restraints weight = 56526.140| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 3.02 r_work: 0.2564 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2567 r_free = 0.2567 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2567 r_free = 0.2567 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 14166 Z= 0.104 Angle : 0.509 11.144 19400 Z= 0.255 Chirality : 0.037 0.164 2193 Planarity : 0.005 0.045 2455 Dihedral : 3.722 34.791 1863 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.21 % Allowed : 23.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.21), residues: 1695 helix: 2.06 (0.15), residues: 1221 sheet: None (None), residues: 0 loop : 0.58 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 71 HIS 0.002 0.001 HIS G 104 PHE 0.012 0.001 PHE K 97 TYR 0.005 0.001 TYR J 132 ARG 0.006 0.000 ARG F 82 Details of bonding type rmsd hydrogen bonds : bond 0.03617 ( 869) hydrogen bonds : angle 4.38088 ( 2580) SS BOND : bond 0.00319 ( 5) SS BOND : angle 3.23685 ( 10) covalent geometry : bond 0.00231 (14161) covalent geometry : angle 0.50409 (19390) *********************** 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 411 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 363 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8489 (tpp-160) cc_final: 0.8261 (tpm170) REVERT: C 76 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6702 (mp) REVERT: D 16 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8585 (mp) REVERT: D 18 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.8510 (t80) REVERT: E 29 ASP cc_start: 0.8997 (m-30) cc_final: 0.8674 (m-30) REVERT: G 22 ASP cc_start: 0.8628 (p0) cc_final: 0.8236 (p0) REVERT: G 82 ARG cc_start: 0.8129 (ttp-110) cc_final: 0.7676 (mtp85) REVERT: F 16 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8583 (mp) REVERT: F 18 PHE cc_start: 0.9130 (OUTLIER) cc_final: 0.8598 (t80) REVERT: F 64 GLU cc_start: 0.7955 (tp30) cc_final: 0.7500 (mt-10) REVERT: K 75 ASN cc_start: 0.8449 (t0) cc_final: 0.8234 (t0) REVERT: J 84 LEU cc_start: 0.8234 (mt) cc_final: 0.7937 (mp) REVERT: L 29 ASP cc_start: 0.9058 (m-30) cc_final: 0.8795 (m-30) REVERT: L 91 THR cc_start: 0.8778 (m) cc_final: 0.8537 (m) outliers start: 48 outliers final: 30 residues processed: 390 average time/residue: 0.2426 time to fit residues: 135.4429 Evaluate side-chains 388 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 353 time to evaluate : 1.557 ------------------------------------------------------------------------------- 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 113 GLU Chi-restraints excluded: chain B residue 117 GLU 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 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 76 LEU 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 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 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 89 VAL Chi-restraints excluded: chain I residue 113 GLU 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 J residue 16 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 49 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 167 optimal weight: 1.9990 chunk 142 optimal weight: 0.3980 chunk 111 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- 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 = 0.3065 r_free = 0.3065 target = 0.091532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.068572 restraints weight = 48375.828| |-----------------------------------------------------------------------------| r_work (start): 0.2638 rms_B_bonded: 2.70 r_work: 0.2443 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2443 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2476 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2476 r_free = 0.2476 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2476 r_free = 0.2476 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2476 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14166 Z= 0.168 Angle : 0.576 11.073 19400 Z= 0.292 Chirality : 0.040 0.164 2193 Planarity : 0.005 0.045 2455 Dihedral : 3.851 34.549 1863 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.54 % Allowed : 23.48 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.21), residues: 1695 helix: 1.99 (0.15), residues: 1223 sheet: None (None), residues: 0 loop : 0.42 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 71 HIS 0.005 0.001 HIS E 47 PHE 0.017 0.001 PHE K 97 TYR 0.007 0.001 TYR I 118 ARG 0.004 0.000 ARG H 127 Details of bonding type rmsd hydrogen bonds : bond 0.04603 ( 869) hydrogen bonds : angle 4.51674 ( 2580) SS BOND : bond 0.00381 ( 5) SS BOND : angle 4.71662 ( 10) covalent geometry : bond 0.00412 (14161) covalent geometry : angle 0.56634 (19390) *********************** 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 413 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 360 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 CYS cc_start: 0.8464 (m) cc_final: 0.8030 (t) REVERT: C 76 LEU cc_start: 0.6967 (OUTLIER) cc_final: 0.6658 (mp) REVERT: D 16 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8650 (mp) REVERT: D 18 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.8466 (t80) REVERT: E 29 ASP cc_start: 0.9063 (m-30) cc_final: 0.8814 (m-30) REVERT: G 22 ASP cc_start: 0.8655 (p0) cc_final: 0.8247 (p0) REVERT: G 82 ARG cc_start: 0.8147 (ttp-110) cc_final: 0.7908 (mtm-85) REVERT: F 16 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8663 (mp) REVERT: F 18 PHE cc_start: 0.9149 (OUTLIER) cc_final: 0.8495 (t80) REVERT: F 64 GLU cc_start: 0.8053 (tp30) cc_final: 0.7557 (mt-10) REVERT: F 96 LYS cc_start: 0.8879 (ptpt) cc_final: 0.8589 (ptmt) REVERT: K 75 ASN cc_start: 0.8443 (t0) cc_final: 0.8219 (t0) REVERT: J 22 ASP cc_start: 0.8637 (p0) cc_final: 0.8247 (p0) REVERT: J 84 LEU cc_start: 0.8216 (mt) cc_final: 0.7908 (mp) REVERT: L 29 ASP cc_start: 0.9067 (m-30) cc_final: 0.8785 (m-30) outliers start: 53 outliers final: 41 residues processed: 390 average time/residue: 0.2507 time to fit residues: 140.7380 Evaluate side-chains 399 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 353 time to evaluate : 1.553 ------------------------------------------------------------------------------- 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 89 VAL 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 76 LEU Chi-restraints excluded: chain C residue 66 MET 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 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 96 LYS 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 65 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 72 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 113 GLU 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 J residue 16 LEU 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 84 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 115 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3143 r_free = 0.3143 target = 0.096383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.074087 restraints weight = 32662.988| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 2.11 r_work: 0.2565 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2431 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2482 r_free = 0.2482 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2482 r_free = 0.2482 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 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 : 0.002 0.044 14166 Z= 0.110 Angle : 0.540 13.816 19400 Z= 0.272 Chirality : 0.037 0.162 2193 Planarity : 0.005 0.043 2455 Dihedral : 3.749 34.340 1863 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.69 % Allowed : 24.52 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.21), residues: 1695 helix: 2.09 (0.15), residues: 1221 sheet: None (None), residues: 0 loop : 0.64 (0.31), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 71 HIS 0.003 0.001 HIS G 104 PHE 0.011 0.001 PHE K 97 TYR 0.005 0.001 TYR A 88 ARG 0.005 0.000 ARG F 82 Details of bonding type rmsd hydrogen bonds : bond 0.03617 ( 869) hydrogen bonds : angle 4.40749 ( 2580) SS BOND : bond 0.00352 ( 5) SS BOND : angle 4.27868 ( 10) covalent geometry : bond 0.00242 (14161) covalent geometry : angle 0.53104 (19390) *********************** 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 395 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 355 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 CYS cc_start: 0.8557 (m) cc_final: 0.8092 (t) REVERT: C 76 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6711 (mp) REVERT: D 18 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8529 (t80) REVERT: E 29 ASP cc_start: 0.9038 (m-30) cc_final: 0.8787 (m-30) REVERT: G 22 ASP cc_start: 0.8795 (p0) cc_final: 0.8361 (p0) REVERT: G 71 TRP cc_start: 0.8311 (t60) cc_final: 0.7884 (t60) REVERT: F 16 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8540 (mp) REVERT: F 18 PHE cc_start: 0.9140 (OUTLIER) cc_final: 0.8612 (t80) REVERT: F 64 GLU cc_start: 0.8148 (tp30) cc_final: 0.7599 (mt-10) REVERT: H 1 MET cc_start: 0.7644 (mtp) cc_final: 0.7195 (ttm) REVERT: K 75 ASN cc_start: 0.8466 (t0) cc_final: 0.8248 (t0) REVERT: J 22 ASP cc_start: 0.8786 (p0) cc_final: 0.8380 (p0) REVERT: J 71 TRP cc_start: 0.8419 (t60) cc_final: 0.8166 (t60) REVERT: J 84 LEU cc_start: 0.8214 (mt) cc_final: 0.7932 (mp) REVERT: L 29 ASP cc_start: 0.9133 (m-30) cc_final: 0.8803 (m-30) REVERT: L 91 THR cc_start: 0.8792 (m) cc_final: 0.8575 (m) outliers start: 40 outliers final: 29 residues processed: 379 average time/residue: 0.2458 time to fit residues: 133.3575 Evaluate side-chains 379 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 346 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 113 GLU 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 C residue 142 THR Chi-restraints excluded: chain D residue 18 PHE 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 G residue 16 LEU Chi-restraints excluded: chain G residue 27 VAL 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 61 CYS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 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 8 GLU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain J residue 16 LEU 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 149 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 13 optimal weight: 0.4980 chunk 81 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3142 r_free = 0.3142 target = 0.096377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.073889 restraints weight = 51499.459| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 2.82 r_work: 0.2551 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14166 Z= 0.108 Angle : 0.550 15.554 19400 Z= 0.273 Chirality : 0.037 0.163 2193 Planarity : 0.005 0.043 2455 Dihedral : 3.688 34.736 1863 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.82 % Allowed : 24.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.21), residues: 1695 helix: 2.27 (0.15), residues: 1195 sheet: None (None), residues: 0 loop : 0.60 (0.30), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 71 HIS 0.003 0.001 HIS J 104 PHE 0.013 0.001 PHE K 97 TYR 0.012 0.001 TYR H 88 ARG 0.007 0.000 ARG F 82 Details of bonding type rmsd hydrogen bonds : bond 0.03519 ( 869) hydrogen bonds : angle 4.39234 ( 2580) SS BOND : bond 0.00271 ( 5) SS BOND : angle 4.02196 ( 10) covalent geometry : bond 0.00240 (14161) covalent geometry : angle 0.54266 (19390) ********************** 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 398 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 356 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 CYS cc_start: 0.8461 (m) cc_final: 0.8003 (t) REVERT: C 76 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6663 (mp) REVERT: D 16 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8529 (mp) REVERT: D 18 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.8505 (t80) REVERT: E 29 ASP cc_start: 0.8951 (m-30) cc_final: 0.8720 (m-30) REVERT: G 22 ASP cc_start: 0.8660 (p0) cc_final: 0.8250 (p0) REVERT: F 16 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8551 (mp) REVERT: F 18 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.8583 (t80) REVERT: F 64 GLU cc_start: 0.8069 (tp30) cc_final: 0.7564 (mt-10) REVERT: H 1 MET cc_start: 0.7597 (mtp) cc_final: 0.7233 (ttm) REVERT: K 75 ASN cc_start: 0.8403 (t0) cc_final: 0.8201 (t0) REVERT: J 22 ASP cc_start: 0.8651 (p0) cc_final: 0.8258 (p0) REVERT: L 4 ASP cc_start: 0.8385 (t0) cc_final: 0.7977 (t0) REVERT: L 29 ASP cc_start: 0.9036 (m-30) cc_final: 0.8690 (m-30) REVERT: L 91 THR cc_start: 0.8790 (m) cc_final: 0.8563 (m) outliers start: 42 outliers final: 31 residues processed: 383 average time/residue: 0.2400 time to fit residues: 132.4572 Evaluate side-chains 380 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 344 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 113 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 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 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 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 61 CYS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 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 8 GLU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 27 VAL 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 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 155 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 158 optimal weight: 0.4980 chunk 98 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 137 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3165 r_free = 0.3165 target = 0.097900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.075137 restraints weight = 37988.771| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 2.29 r_work: 0.2599 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14166 Z= 0.108 Angle : 0.555 13.729 19400 Z= 0.274 Chirality : 0.038 0.156 2193 Planarity : 0.005 0.042 2455 Dihedral : 3.646 34.072 1863 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.49 % Allowed : 24.85 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.21), residues: 1695 helix: 2.28 (0.15), residues: 1190 sheet: None (None), residues: 0 loop : 0.68 (0.30), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 71 HIS 0.003 0.001 HIS J 104 PHE 0.012 0.001 PHE K 97 TYR 0.008 0.001 TYR J 132 ARG 0.006 0.000 ARG F 82 Details of bonding type rmsd hydrogen bonds : bond 0.03355 ( 869) hydrogen bonds : angle 4.38363 ( 2580) SS BOND : bond 0.00271 ( 5) SS BOND : angle 3.56200 ( 10) covalent geometry : bond 0.00239 (14161) covalent geometry : angle 0.54972 (19390) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7427.07 seconds wall clock time: 129 minutes 11.73 seconds (7751.73 seconds total)