Starting phenix.real_space_refine on Thu Jul 31 13:13:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g6v_29785/07_2025/8g6v_29785.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g6v_29785/07_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_29785/07_2025/8g6v_29785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g6v_29785/07_2025/8g6v_29785.map" model { file = "/net/cci-nas-00/data/ceres_data/8g6v_29785/07_2025/8g6v_29785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g6v_29785/07_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 10.21, per 1000 atoms: 0.74 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: 3.09 Conformation dependent library (CDL) restraints added in 1.9 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: 3.77 Time building geometry restraints manager: 3.70 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: 6.440 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 33.290 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.010 ------------------------------------------------------------------------------- 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 : 1.578 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: 0.2601 time to fit residues: 139.8452 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 : 1.793 ------------------------------------------------------------------------------- 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 = 41)----------------| | 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: 0.2556 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2547 r_free = 0.2547 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 = 0.2547 r_free = 0.2547 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 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 : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8462 (tpp-160) cc_final: 0.8140 (tpm170) REVERT: D 82 ARG cc_start: 0.8243 (mtm-85) cc_final: 0.8003 (mtm110) REVERT: E 29 ASP cc_start: 0.9000 (m-30) cc_final: 0.8627 (m-30) REVERT: G 82 ARG cc_start: 0.8082 (ttp-110) cc_final: 0.7631 (mtp85) REVERT: F 18 PHE cc_start: 0.9141 (OUTLIER) cc_final: 0.8458 (t80) REVERT: F 64 GLU cc_start: 0.8007 (tp30) cc_final: 0.7724 (mt-10) REVERT: F 96 LYS cc_start: 0.8858 (ptpt) cc_final: 0.8505 (ptmt) REVERT: I 78 ASP cc_start: 0.7385 (t70) cc_final: 0.7095 (t70) REVERT: K 75 ASN cc_start: 0.8382 (t0) cc_final: 0.8174 (t0) outliers start: 36 outliers final: 16 residues processed: 383 average time/residue: 0.2519 time to fit residues: 138.2384 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 : 1.587 ------------------------------------------------------------------------------- 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: 1.9990 chunk 121 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3118 r_free = 0.3118 target = 0.095181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.072167 restraints weight = 42655.462| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 2.56 r_work: 0.2536 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2513 r_free = 0.2513 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2513 r_free = 0.2513 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14166 Z= 0.115 Angle : 0.507 11.342 19400 Z= 0.252 Chirality : 0.038 0.145 2193 Planarity : 0.005 0.063 2455 Dihedral : 3.754 34.868 1863 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.15 % Allowed : 22.69 % Favored : 74.16 % 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: 2.17 (0.21), residues: 1695 helix: 1.85 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : 0.51 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 71 HIS 0.004 0.001 HIS J 104 PHE 0.016 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 0.04088 ( 869) hydrogen bonds : angle 4.38277 ( 2580) SS BOND : bond 0.00361 ( 5) SS BOND : angle 2.29312 ( 10) covalent geometry : bond 0.00263 (14161) covalent geometry : angle 0.50468 (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 408 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 361 time to evaluate : 3.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8429 (tpp-160) cc_final: 0.8047 (tpm170) REVERT: G 77 GLU cc_start: 0.5999 (pm20) cc_final: 0.5719 (pm20) REVERT: G 82 ARG cc_start: 0.8063 (ttp-110) cc_final: 0.7652 (mtp85) REVERT: F 18 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.8449 (t80) REVERT: F 64 GLU cc_start: 0.8027 (tp30) cc_final: 0.7599 (mt-10) REVERT: F 96 LYS cc_start: 0.8854 (ptpt) cc_final: 0.8492 (ptmt) REVERT: K 75 ASN cc_start: 0.8418 (t0) cc_final: 0.8195 (t0) outliers start: 47 outliers final: 32 residues processed: 385 average time/residue: 0.3609 time to fit residues: 201.5019 Evaluate side-chains 384 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 351 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 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 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 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 chunk 70 optimal weight: 0.0970 chunk 34 optimal weight: 9.9990 chunk 126 optimal weight: 0.2980 chunk 154 optimal weight: 0.6980 chunk 143 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3144 r_free = 0.3144 target = 0.096751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.074109 restraints weight = 36882.962| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 2.24 r_work: 0.2581 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2448 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2467 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2467 r_free = 0.2467 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2467 r_free = 0.2467 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2467 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14166 Z= 0.099 Angle : 0.485 11.475 19400 Z= 0.241 Chirality : 0.036 0.149 2193 Planarity : 0.005 0.054 2455 Dihedral : 3.646 34.186 1863 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.21 % Allowed : 22.43 % Favored : 74.36 % 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: 2.37 (0.21), residues: 1695 helix: 1.99 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : 0.61 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 71 HIS 0.003 0.001 HIS J 104 PHE 0.013 0.001 PHE K 97 TYR 0.005 0.001 TYR I 118 ARG 0.003 0.000 ARG H 127 Details of bonding type rmsd hydrogen bonds : bond 0.03590 ( 869) hydrogen bonds : angle 4.32062 ( 2580) SS BOND : bond 0.00548 ( 5) SS BOND : angle 2.16833 ( 10) covalent geometry : bond 0.00214 (14161) covalent geometry : angle 0.48267 (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 410 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 362 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8620 (tpp-160) cc_final: 0.8221 (tpm170) REVERT: E 29 ASP cc_start: 0.9111 (m-30) cc_final: 0.8847 (m-30) REVERT: G 77 GLU cc_start: 0.6455 (pm20) cc_final: 0.6220 (pm20) REVERT: G 82 ARG cc_start: 0.8103 (ttp-110) cc_final: 0.7580 (mtp85) REVERT: F 18 PHE cc_start: 0.9159 (OUTLIER) cc_final: 0.8492 (t80) REVERT: F 64 GLU cc_start: 0.8149 (tp30) cc_final: 0.7659 (mt-10) REVERT: K 75 ASN cc_start: 0.8465 (t0) cc_final: 0.8253 (t0) REVERT: J 66 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8676 (mmm) REVERT: J 96 LYS cc_start: 0.8799 (ptmt) cc_final: 0.8598 (ptmt) REVERT: L 29 ASP cc_start: 0.9163 (m-30) cc_final: 0.8892 (m-30) REVERT: L 77 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7350 (pm20) REVERT: L 91 THR cc_start: 0.8758 (m) cc_final: 0.8507 (m) outliers start: 48 outliers final: 30 residues processed: 389 average time/residue: 0.3418 time to fit residues: 193.3019 Evaluate side-chains 384 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 351 time to evaluate : 2.638 ------------------------------------------------------------------------------- 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 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 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 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 16 LEU Chi-restraints excluded: chain K residue 74 VAL 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: 4.9990 chunk 35 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 126 optimal weight: 0.0670 chunk 45 optimal weight: 2.9990 chunk 159 optimal weight: 7.9990 chunk 125 optimal weight: 0.0370 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 ASN F 90 ASN J 90 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.097510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.074543 restraints weight = 40798.237| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 2.36 r_work: 0.2584 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2452 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2452 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2434 r_free = 0.2434 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2434 r_free = 0.2434 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14166 Z= 0.102 Angle : 0.484 11.164 19400 Z= 0.241 Chirality : 0.037 0.150 2193 Planarity : 0.005 0.050 2455 Dihedral : 3.612 35.473 1863 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.21 % Allowed : 22.89 % Favored : 73.90 % 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: 2.49 (0.21), residues: 1695 helix: 2.08 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : 0.67 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 71 HIS 0.003 0.001 HIS J 104 PHE 0.014 0.001 PHE K 97 TYR 0.005 0.001 TYR J 132 ARG 0.004 0.000 ARG F 82 Details of bonding type rmsd hydrogen bonds : bond 0.03547 ( 869) hydrogen bonds : angle 4.33160 ( 2580) SS BOND : bond 0.00300 ( 5) SS BOND : angle 2.35389 ( 10) covalent geometry : bond 0.00229 (14161) covalent geometry : angle 0.48114 (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 411 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 363 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8660 (tpp-160) cc_final: 0.8301 (tpm170) REVERT: C 76 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6880 (mp) REVERT: E 29 ASP cc_start: 0.9120 (m-30) cc_final: 0.8841 (m-30) REVERT: G 77 GLU cc_start: 0.6482 (pm20) cc_final: 0.6243 (pm20) REVERT: G 82 ARG cc_start: 0.8111 (ttp-110) cc_final: 0.7601 (mtp85) REVERT: F 18 PHE cc_start: 0.9157 (OUTLIER) cc_final: 0.8495 (t80) REVERT: F 64 GLU cc_start: 0.8183 (tp30) cc_final: 0.7629 (mt-10) REVERT: K 75 ASN cc_start: 0.8479 (t0) cc_final: 0.8266 (t0) REVERT: J 61 CYS cc_start: 0.8396 (t) cc_final: 0.7955 (t) REVERT: L 29 ASP cc_start: 0.9152 (m-30) cc_final: 0.8876 (m-30) REVERT: L 77 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7355 (pm20) REVERT: L 91 THR cc_start: 0.8849 (m) cc_final: 0.8608 (m) outliers start: 48 outliers final: 37 residues processed: 388 average time/residue: 0.3703 time to fit residues: 209.4276 Evaluate side-chains 392 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 352 time to evaluate : 2.775 ------------------------------------------------------------------------------- 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 6 TYR Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain D residue 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 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 57 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 134 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 148 optimal weight: 10.0000 chunk 137 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.093829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.071309 restraints weight = 40513.404| |-----------------------------------------------------------------------------| r_work (start): 0.2656 rms_B_bonded: 2.41 r_work: 0.2488 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2540 r_free = 0.2540 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2540 r_free = 0.2540 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1337 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= 0.142 Angle : 0.529 11.078 19400 Z= 0.267 Chirality : 0.039 0.159 2193 Planarity : 0.005 0.048 2455 Dihedral : 3.746 33.072 1863 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.41 % Allowed : 23.41 % Favored : 73.18 % 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: 2.39 (0.21), residues: 1695 helix: 2.02 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : 0.56 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 71 HIS 0.005 0.001 HIS E 47 PHE 0.016 0.001 PHE K 97 TYR 0.009 0.001 TYR K 88 ARG 0.005 0.000 ARG F 82 Details of bonding type rmsd hydrogen bonds : bond 0.04410 ( 869) hydrogen bonds : angle 4.44500 ( 2580) SS BOND : bond 0.00393 ( 5) SS BOND : angle 2.71340 ( 10) covalent geometry : bond 0.00342 (14161) covalent geometry : angle 0.52532 (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 418 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 367 time to evaluate : 4.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8524 (tpp-160) cc_final: 0.8185 (tpm170) REVERT: B 61 CYS cc_start: 0.8416 (m) cc_final: 0.7974 (t) REVERT: C 76 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6729 (mp) REVERT: D 18 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8429 (t80) REVERT: E 29 ASP cc_start: 0.9003 (m-30) cc_final: 0.8708 (m-30) REVERT: G 82 ARG cc_start: 0.8143 (ttp-110) cc_final: 0.7642 (mtp85) REVERT: F 18 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.8475 (t80) REVERT: F 64 GLU cc_start: 0.7982 (tp30) cc_final: 0.7529 (mt-10) REVERT: K 75 ASN cc_start: 0.8453 (t0) cc_final: 0.8228 (t0) REVERT: J 84 LEU cc_start: 0.8256 (mt) cc_final: 0.8051 (mp) REVERT: J 96 LYS cc_start: 0.8698 (ptmt) cc_final: 0.8484 (ptmt) REVERT: L 29 ASP cc_start: 0.9052 (m-30) cc_final: 0.8781 (m-30) outliers start: 51 outliers final: 40 residues processed: 392 average time/residue: 0.4544 time to fit residues: 259.2222 Evaluate side-chains 402 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 359 time to evaluate : 3.189 ------------------------------------------------------------------------------- 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 46 GLU 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 76 LEU Chi-restraints excluded: chain C residue 142 THR 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 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 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 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 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: 8.9990 chunk 4 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 155 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 111 optimal weight: 30.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- 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 = 0.3090 r_free = 0.3090 target = 0.093153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.070623 restraints weight = 56871.092| |-----------------------------------------------------------------------------| r_work (start): 0.2624 rms_B_bonded: 2.97 r_work: 0.2433 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2433 ------------------------------------------------------------------------------- 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: 0.8844 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14166 Z= 0.180 Angle : 0.580 13.190 19400 Z= 0.292 Chirality : 0.041 0.163 2193 Planarity : 0.005 0.047 2455 Dihedral : 3.944 33.185 1863 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.74 % Allowed : 23.48 % 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: 2.15 (0.21), residues: 1695 helix: 1.90 (0.15), residues: 1224 sheet: None (None), residues: 0 loop : 0.28 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 71 HIS 0.007 0.001 HIS E 47 PHE 0.017 0.001 PHE K 97 TYR 0.009 0.001 TYR K 88 ARG 0.004 0.000 ARG H 127 Details of bonding type rmsd hydrogen bonds : bond 0.05095 ( 869) hydrogen bonds : angle 4.57042 ( 2580) SS BOND : bond 0.00462 ( 5) SS BOND : angle 3.40960 ( 10) covalent geometry : bond 0.00446 (14161) covalent geometry : angle 0.57505 (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 422 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 366 time to evaluate : 2.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8525 (tpp-160) cc_final: 0.8196 (tpp-160) REVERT: B 61 CYS cc_start: 0.8467 (m) cc_final: 0.8081 (t) REVERT: C 76 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6698 (mp) REVERT: D 18 PHE cc_start: 0.9086 (OUTLIER) cc_final: 0.8498 (t80) REVERT: E 29 ASP cc_start: 0.9045 (m-30) cc_final: 0.8736 (m-30) REVERT: G 22 ASP cc_start: 0.8634 (p0) cc_final: 0.8235 (p0) REVERT: G 82 ARG cc_start: 0.8186 (ttp-110) cc_final: 0.7662 (mtp85) REVERT: F 16 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8773 (mp) REVERT: F 18 PHE cc_start: 0.9153 (OUTLIER) cc_final: 0.8510 (t80) REVERT: F 64 GLU cc_start: 0.8011 (tp30) cc_final: 0.7543 (mt-10) REVERT: K 75 ASN cc_start: 0.8495 (t0) cc_final: 0.8252 (t0) REVERT: J 22 ASP cc_start: 0.8610 (p0) cc_final: 0.8229 (p0) REVERT: J 84 LEU cc_start: 0.8283 (mt) cc_final: 0.8016 (mp) outliers start: 56 outliers final: 38 residues processed: 393 average time/residue: 0.2967 time to fit residues: 168.2526 Evaluate side-chains 400 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 358 time to evaluate : 1.380 ------------------------------------------------------------------------------- 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 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 76 LEU Chi-restraints excluded: chain C residue 142 THR 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 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 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 K residue 8 GLU Chi-restraints excluded: chain K residue 67 THR 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 139 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 49 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 167 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 = 0.3072 r_free = 0.3072 target = 0.092772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.068918 restraints weight = 46659.486| |-----------------------------------------------------------------------------| r_work (start): 0.2597 rms_B_bonded: 2.76 r_work: 0.2419 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2430 r_free = 0.2430 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2430 r_free = 0.2430 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14166 Z= 0.183 Angle : 0.590 11.847 19400 Z= 0.297 Chirality : 0.041 0.165 2193 Planarity : 0.005 0.047 2455 Dihedral : 4.015 32.876 1863 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.67 % Allowed : 23.54 % 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: 2.09 (0.21), residues: 1695 helix: 1.87 (0.15), residues: 1224 sheet: None (None), residues: 0 loop : 0.20 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 71 HIS 0.007 0.001 HIS E 47 PHE 0.017 0.001 PHE G 18 TYR 0.009 0.001 TYR K 88 ARG 0.005 0.000 ARG F 82 Details of bonding type rmsd hydrogen bonds : bond 0.05141 ( 869) hydrogen bonds : angle 4.59360 ( 2580) SS BOND : bond 0.00400 ( 5) SS BOND : angle 4.35006 ( 10) covalent geometry : bond 0.00450 (14161) covalent geometry : angle 0.58146 (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 417 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 362 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 CYS cc_start: 0.8422 (m) cc_final: 0.8093 (t) REVERT: C 76 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6623 (mp) REVERT: D 18 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.8389 (t80) REVERT: E 29 ASP cc_start: 0.9036 (m-30) cc_final: 0.8733 (m-30) REVERT: G 22 ASP cc_start: 0.8648 (p0) cc_final: 0.8218 (p0) REVERT: F 16 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8750 (mp) REVERT: F 18 PHE cc_start: 0.9156 (OUTLIER) cc_final: 0.8502 (t80) REVERT: F 64 GLU cc_start: 0.8074 (tp30) cc_final: 0.7547 (mt-10) REVERT: I 14 GLU cc_start: 0.8813 (mp0) cc_final: 0.8551 (mp0) REVERT: K 39 ARG cc_start: 0.8351 (ttm-80) cc_final: 0.8089 (ttm-80) REVERT: K 75 ASN cc_start: 0.8505 (t0) cc_final: 0.8245 (t0) REVERT: J 22 ASP cc_start: 0.8656 (p0) cc_final: 0.8251 (p0) REVERT: J 84 LEU cc_start: 0.8247 (mt) cc_final: 0.7931 (mp) outliers start: 55 outliers final: 44 residues processed: 389 average time/residue: 0.2559 time to fit residues: 142.7927 Evaluate side-chains 406 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 358 time to evaluate : 1.547 ------------------------------------------------------------------------------- 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 46 GLU 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 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 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 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 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 K residue 8 GLU Chi-restraints excluded: chain K residue 67 THR 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 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: 5.9990 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 136 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.3104 r_free = 0.3104 target = 0.094094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.071570 restraints weight = 32706.450| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 2.11 r_work: 0.2513 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2380 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2394 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2394 r_free = 0.2394 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2394 r_free = 0.2394 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2394 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14166 Z= 0.127 Angle : 0.555 11.756 19400 Z= 0.280 Chirality : 0.038 0.162 2193 Planarity : 0.005 0.046 2455 Dihedral : 3.904 34.089 1863 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.21 % Allowed : 24.39 % Favored : 72.39 % 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: 2.31 (0.21), residues: 1695 helix: 1.99 (0.15), residues: 1219 sheet: None (None), residues: 0 loop : 0.45 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 71 HIS 0.005 0.001 HIS E 47 PHE 0.013 0.001 PHE K 97 TYR 0.008 0.001 TYR K 88 ARG 0.005 0.000 ARG F 82 Details of bonding type rmsd hydrogen bonds : bond 0.04314 ( 869) hydrogen bonds : angle 4.49207 ( 2580) SS BOND : bond 0.00411 ( 5) SS BOND : angle 3.86979 ( 10) covalent geometry : bond 0.00293 (14161) covalent geometry : angle 0.54845 (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 404 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 356 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 CYS cc_start: 0.8588 (m) cc_final: 0.8226 (t) REVERT: C 76 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6671 (mp) REVERT: D 18 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.8493 (t80) REVERT: D 84 LEU cc_start: 0.8145 (mt) cc_final: 0.7929 (mp) REVERT: E 29 ASP cc_start: 0.9050 (m-30) cc_final: 0.8792 (m-30) REVERT: G 22 ASP cc_start: 0.8790 (p0) cc_final: 0.8346 (p0) REVERT: F 16 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8677 (mp) REVERT: F 18 PHE cc_start: 0.9157 (OUTLIER) cc_final: 0.8518 (t80) REVERT: F 64 GLU cc_start: 0.8164 (tp30) cc_final: 0.7638 (mt-10) REVERT: K 75 ASN cc_start: 0.8528 (t0) cc_final: 0.8289 (t0) REVERT: J 22 ASP cc_start: 0.8787 (p0) cc_final: 0.8382 (p0) REVERT: J 84 LEU cc_start: 0.8236 (mt) cc_final: 0.7920 (mp) REVERT: L 29 ASP cc_start: 0.9150 (m-30) cc_final: 0.8806 (m-30) outliers start: 48 outliers final: 36 residues processed: 383 average time/residue: 0.2606 time to fit residues: 143.8618 Evaluate side-chains 392 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 352 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 GLU 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 B residue 139 ILE Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain C residue 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 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 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 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 139 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 149 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 13 optimal weight: 0.0570 chunk 81 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- 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 = 0.3076 r_free = 0.3076 target = 0.092435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.069291 restraints weight = 51606.256| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 2.77 r_work: 0.2487 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2553 r_free = 0.2553 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2553 r_free = 0.2553 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14166 Z= 0.108 Angle : 0.539 12.759 19400 Z= 0.270 Chirality : 0.037 0.154 2193 Planarity : 0.005 0.045 2455 Dihedral : 3.775 34.673 1863 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.82 % Allowed : 24.79 % Favored : 72.39 % 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: 2.57 (0.21), residues: 1695 helix: 2.24 (0.15), residues: 1193 sheet: None (None), residues: 0 loop : 0.49 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 71 HIS 0.003 0.001 HIS E 47 PHE 0.012 0.001 PHE K 97 TYR 0.013 0.001 TYR H 88 ARG 0.006 0.000 ARG F 82 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 869) hydrogen bonds : angle 4.38386 ( 2580) SS BOND : bond 0.00420 ( 5) SS BOND : angle 1.58039 ( 10) covalent geometry : bond 0.00233 (14161) covalent geometry : angle 0.53819 (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 404 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 362 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 CYS cc_start: 0.8494 (m) cc_final: 0.8119 (t) REVERT: C 76 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6617 (mp) REVERT: D 18 PHE cc_start: 0.9063 (OUTLIER) cc_final: 0.8518 (t80) REVERT: D 84 LEU cc_start: 0.8136 (mt) cc_final: 0.7922 (mp) REVERT: E 29 ASP cc_start: 0.8944 (m-30) cc_final: 0.8692 (m-30) REVERT: G 22 ASP cc_start: 0.8686 (p0) cc_final: 0.8267 (p0) REVERT: F 16 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8561 (mp) REVERT: F 18 PHE cc_start: 0.9119 (OUTLIER) cc_final: 0.8598 (t80) REVERT: F 64 GLU cc_start: 0.8093 (tp30) cc_final: 0.7569 (mt-10) REVERT: K 75 ASN cc_start: 0.8374 (t0) cc_final: 0.8137 (t0) REVERT: J 22 ASP cc_start: 0.8651 (p0) cc_final: 0.8255 (p0) REVERT: J 71 TRP cc_start: 0.8377 (t60) cc_final: 0.7960 (t60) REVERT: J 84 LEU cc_start: 0.8194 (mt) cc_final: 0.7906 (mp) outliers start: 42 outliers final: 30 residues processed: 387 average time/residue: 0.2478 time to fit residues: 138.1920 Evaluate side-chains 385 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 351 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 GLU 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 B residue 139 ILE Chi-restraints excluded: chain A residue 6 TYR 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 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 66 MET Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain 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: 0.6980 chunk 48 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 54 optimal weight: 0.1980 chunk 12 optimal weight: 9.9990 chunk 158 optimal weight: 0.7980 chunk 98 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 = 0.3134 r_free = 0.3134 target = 0.096003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.073076 restraints weight = 37857.551| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 2.29 r_work: 0.2539 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2530 r_free = 0.2530 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2530 r_free = 0.2530 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14166 Z= 0.114 Angle : 0.548 12.411 19400 Z= 0.276 Chirality : 0.038 0.168 2193 Planarity : 0.005 0.044 2455 Dihedral : 3.731 34.064 1863 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.62 % Allowed : 24.98 % Favored : 72.39 % 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: 2.62 (0.21), residues: 1695 helix: 2.26 (0.15), residues: 1193 sheet: None (None), residues: 0 loop : 0.55 (0.30), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 71 HIS 0.004 0.001 HIS E 47 PHE 0.014 0.001 PHE K 97 TYR 0.010 0.001 TYR J 132 ARG 0.005 0.000 ARG F 82 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 869) hydrogen bonds : angle 4.39231 ( 2580) SS BOND : bond 0.00392 ( 5) SS BOND : angle 1.44096 ( 10) covalent geometry : bond 0.00258 (14161) covalent geometry : angle 0.54765 (19390) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8671.01 seconds wall clock time: 161 minutes 28.07 seconds (9688.07 seconds total)