Starting phenix.real_space_refine on Mon Dec 30 16:14:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g6v_29785/12_2024/8g6v_29785.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g6v_29785/12_2024/8g6v_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_29785/12_2024/8g6v_29785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g6v_29785/12_2024/8g6v_29785.map" model { file = "/net/cci-nas-00/data/ceres_data/8g6v_29785/12_2024/8g6v_29785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g6v_29785/12_2024/8g6v_29785.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 8932 2.51 5 N 2248 2.21 5 O 2484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13736 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1136 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 11, 'TRANS': 130} Chain: "A" Number of atoms: 1155 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 143, 1144 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Conformer: "B" Number of residues, atoms: 143, 1144 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} bond proxies already assigned to first conformer: 1167 Chain: "C" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1151 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 12, 'TRANS': 131} Chain: "D" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1144 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "E" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1151 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 12, 'TRANS': 131} Chain: "G" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1144 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "F" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1144 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "H" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1151 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 12, 'TRANS': 131} Chain: "I" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1129 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 11, 'TRANS': 129} Chain: "K" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1136 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 11, 'TRANS': 130} Chain: "J" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1144 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "L" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1151 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 12, 'TRANS': 131} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 112 " occ=0.12 ... (20 atoms not shown) pdb=" NH2BARG A 112 " occ=0.88 Time building chain proxies: 9.88, per 1000 atoms: 0.72 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: 3.04 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: 1.21 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: 3.97 Time building geometry restraints manager: 3.62 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: 5.100 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: 0.110 Set scattering table: 0.130 Process input model: 32.500 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.010 ------------------------------------------------------------------------------- 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 14161 Z= 0.193 Angle : 0.596 15.996 19390 Z= 0.312 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 *********************** 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 : 1.486 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: 0.2689 time to fit residues: 144.2978 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 : 1.414 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 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 14161 Z= 0.167 Angle : 0.520 10.885 19390 Z= 0.259 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 *********************** 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 : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8388 (tpp-160) cc_final: 0.8061 (tpm170) REVERT: D 82 ARG cc_start: 0.8217 (mtm-85) cc_final: 0.7945 (mtm110) REVERT: E 29 ASP cc_start: 0.9054 (m-30) cc_final: 0.8668 (m-30) REVERT: G 82 ARG cc_start: 0.8059 (ttp-110) cc_final: 0.7621 (mtp85) REVERT: F 18 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.8491 (t80) REVERT: F 64 GLU cc_start: 0.7830 (tp30) cc_final: 0.7604 (mt-10) REVERT: F 96 LYS cc_start: 0.8860 (ptpt) cc_final: 0.8407 (ptmt) REVERT: I 78 ASP cc_start: 0.7364 (t70) cc_final: 0.7053 (t70) REVERT: K 75 ASN cc_start: 0.8350 (t0) cc_final: 0.8132 (t0) outliers start: 36 outliers final: 16 residues processed: 383 average time/residue: 0.2666 time to fit residues: 146.4588 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 : 1.459 ------------------------------------------------------------------------------- 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 84 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 126 optimal weight: 0.3980 chunk 103 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 chunk 165 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14161 Z= 0.155 Angle : 0.498 11.276 19390 Z= 0.247 Chirality : 0.037 0.144 2193 Planarity : 0.005 0.062 2455 Dihedral : 3.733 35.013 1863 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.95 % Allowed : 22.69 % 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: 2.19 (0.21), residues: 1695 helix: 1.86 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : 0.53 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 71 HIS 0.003 0.001 HIS J 104 PHE 0.015 0.001 PHE K 97 TYR 0.007 0.001 TYR K 88 ARG 0.003 0.000 ARG H 127 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 360 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8399 (tpp-160) cc_final: 0.8021 (tpm170) REVERT: G 77 GLU cc_start: 0.5919 (pm20) cc_final: 0.5674 (pm20) REVERT: G 82 ARG cc_start: 0.8071 (ttp-110) cc_final: 0.7671 (mtp85) REVERT: F 18 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8501 (t80) REVERT: F 64 GLU cc_start: 0.7813 (tp30) cc_final: 0.7480 (mt-10) REVERT: F 96 LYS cc_start: 0.8836 (ptpt) cc_final: 0.8382 (ptmt) REVERT: K 75 ASN cc_start: 0.8399 (t0) cc_final: 0.8166 (t0) outliers start: 44 outliers final: 27 residues processed: 384 average time/residue: 0.2781 time to fit residues: 154.2927 Evaluate side-chains 377 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 349 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 145 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14161 Z= 0.168 Angle : 0.499 11.526 19390 Z= 0.248 Chirality : 0.037 0.144 2193 Planarity : 0.005 0.054 2455 Dihedral : 3.690 33.749 1863 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.61 % Allowed : 22.30 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.21), residues: 1695 helix: 1.96 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : 0.55 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 71 HIS 0.004 0.001 HIS G 104 PHE 0.015 0.001 PHE K 97 TYR 0.006 0.001 TYR I 118 ARG 0.003 0.000 ARG H 127 *********************** 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 417 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 363 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8385 (tpp-160) cc_final: 0.7997 (tpm170) REVERT: B 61 CYS cc_start: 0.8361 (m) cc_final: 0.7928 (t) REVERT: E 29 ASP cc_start: 0.9046 (m-30) cc_final: 0.8731 (m-30) REVERT: G 82 ARG cc_start: 0.8087 (ttp-110) cc_final: 0.7584 (mtp85) REVERT: F 18 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8502 (t80) REVERT: F 64 GLU cc_start: 0.7773 (tp30) cc_final: 0.7471 (mt-10) REVERT: F 96 LYS cc_start: 0.8846 (ptpt) cc_final: 0.8347 (ptmt) REVERT: K 75 ASN cc_start: 0.8437 (t0) cc_final: 0.8206 (t0) REVERT: J 96 LYS cc_start: 0.8757 (ptmt) cc_final: 0.8504 (ptmt) REVERT: L 29 ASP cc_start: 0.9094 (m-30) cc_final: 0.8772 (m-30) REVERT: L 77 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7224 (pm20) REVERT: L 91 THR cc_start: 0.8702 (m) cc_final: 0.8432 (m) outliers start: 54 outliers final: 36 residues processed: 392 average time/residue: 0.2608 time to fit residues: 146.7487 Evaluate side-chains 394 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 356 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 82 ARG Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 107 CYS Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain K residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 2 optimal weight: 0.0010 chunk 120 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 138 optimal weight: 0.9980 chunk 112 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.3992 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14161 Z= 0.197 Angle : 0.509 11.123 19390 Z= 0.255 Chirality : 0.038 0.151 2193 Planarity : 0.005 0.050 2455 Dihedral : 3.739 34.897 1863 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.61 % Allowed : 22.82 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (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: 2.33 (0.21), residues: 1695 helix: 1.99 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : 0.49 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 71 HIS 0.004 0.001 HIS E 47 PHE 0.016 0.001 PHE K 97 TYR 0.007 0.001 TYR K 88 ARG 0.004 0.000 ARG F 82 *********************** 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 420 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 366 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8397 (tpp-160) cc_final: 0.8011 (tpm170) REVERT: B 61 CYS cc_start: 0.8352 (m) cc_final: 0.7954 (t) REVERT: C 76 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6715 (mp) REVERT: D 18 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.8350 (t80) REVERT: E 29 ASP cc_start: 0.9061 (m-30) cc_final: 0.8720 (m-30) REVERT: G 77 GLU cc_start: 0.6046 (pm20) cc_final: 0.5836 (pm20) REVERT: G 82 ARG cc_start: 0.8096 (ttp-110) cc_final: 0.7601 (mtp85) REVERT: F 18 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8511 (t80) REVERT: F 64 GLU cc_start: 0.7775 (tp30) cc_final: 0.7418 (mt-10) REVERT: F 96 LYS cc_start: 0.8860 (ptpt) cc_final: 0.8351 (ptmt) REVERT: K 75 ASN cc_start: 0.8442 (t0) cc_final: 0.8208 (t0) REVERT: L 29 ASP cc_start: 0.9079 (m-30) cc_final: 0.8775 (m-30) REVERT: L 77 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7260 (pm20) REVERT: L 91 THR cc_start: 0.8701 (m) cc_final: 0.8431 (m) outliers start: 54 outliers final: 42 residues processed: 395 average time/residue: 0.2637 time to fit residues: 149.2187 Evaluate side-chains 402 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 356 time to evaluate : 1.611 ------------------------------------------------------------------------------- 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 6 TYR Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 82 ARG Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 107 CYS Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain 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 54 optimal weight: 0.5980 chunk 146 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 0.0030 overall best weight: 2.7196 ------------------------------------------------------------------------------- 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 K 47 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14161 Z= 0.215 Angle : 0.523 11.162 19390 Z= 0.264 Chirality : 0.039 0.159 2193 Planarity : 0.005 0.047 2455 Dihedral : 3.795 33.212 1863 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.80 % Allowed : 22.82 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.21), residues: 1695 helix: 1.99 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : 0.44 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 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 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 364 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8400 (tpp-160) cc_final: 0.8036 (tpm170) REVERT: B 61 CYS cc_start: 0.8347 (m) cc_final: 0.7973 (t) REVERT: C 76 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.6682 (mp) REVERT: D 18 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8465 (t80) REVERT: E 29 ASP cc_start: 0.9042 (m-30) cc_final: 0.8703 (m-30) REVERT: G 82 ARG cc_start: 0.8130 (ttp-110) cc_final: 0.7637 (mtp85) REVERT: F 18 PHE cc_start: 0.9180 (OUTLIER) cc_final: 0.8518 (t80) REVERT: F 64 GLU cc_start: 0.7754 (tp30) cc_final: 0.7404 (mt-10) REVERT: F 96 LYS cc_start: 0.8847 (ptpt) cc_final: 0.8423 (ptmt) REVERT: K 75 ASN cc_start: 0.8441 (t0) cc_final: 0.8193 (t0) REVERT: J 61 CYS cc_start: 0.7605 (t) cc_final: 0.6965 (t) REVERT: J 96 LYS cc_start: 0.8766 (ptmt) cc_final: 0.8521 (ptmt) REVERT: L 29 ASP cc_start: 0.9082 (m-30) cc_final: 0.8749 (m-30) outliers start: 57 outliers final: 43 residues processed: 396 average time/residue: 0.2623 time to fit residues: 148.9948 Evaluate side-chains 403 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 357 time to evaluate : 1.766 ------------------------------------------------------------------------------- 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 16 LEU Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 82 ARG Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 107 CYS Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain 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 156 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 98 optimal weight: 0.8980 chunk 74 optimal weight: 50.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14161 Z= 0.245 Angle : 0.550 11.078 19390 Z= 0.277 Chirality : 0.040 0.163 2193 Planarity : 0.005 0.046 2455 Dihedral : 3.880 33.499 1863 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.93 % Allowed : 23.02 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (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: 2.24 (0.21), residues: 1695 helix: 1.96 (0.15), residues: 1223 sheet: None (None), residues: 0 loop : 0.36 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 71 HIS 0.006 0.001 HIS E 47 PHE 0.016 0.001 PHE K 97 TYR 0.008 0.001 TYR K 88 ARG 0.004 0.000 ARG J 28 *********************** 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 423 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 364 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8402 (mp0) REVERT: B 61 CYS cc_start: 0.8352 (m) cc_final: 0.7963 (t) REVERT: C 76 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6663 (mp) REVERT: D 16 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8654 (mp) REVERT: D 18 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8502 (t80) REVERT: E 29 ASP cc_start: 0.9038 (m-30) cc_final: 0.8713 (m-30) REVERT: G 22 ASP cc_start: 0.8682 (p0) cc_final: 0.8270 (p0) REVERT: G 82 ARG cc_start: 0.8140 (ttp-110) cc_final: 0.7885 (mtm-85) REVERT: F 18 PHE cc_start: 0.9185 (OUTLIER) cc_final: 0.8524 (t80) REVERT: F 64 GLU cc_start: 0.7764 (tp30) cc_final: 0.7397 (mt-10) REVERT: F 96 LYS cc_start: 0.8887 (ptpt) cc_final: 0.8461 (ptmt) REVERT: K 75 ASN cc_start: 0.8444 (t0) cc_final: 0.8193 (t0) REVERT: J 22 ASP cc_start: 0.8617 (p0) cc_final: 0.8232 (p0) REVERT: J 84 LEU cc_start: 0.8271 (mt) cc_final: 0.7938 (mp) REVERT: J 96 LYS cc_start: 0.8729 (ptmt) cc_final: 0.8511 (ptmt) REVERT: L 29 ASP cc_start: 0.9074 (m-30) cc_final: 0.8746 (m-30) outliers start: 59 outliers final: 46 residues processed: 397 average time/residue: 0.2871 time to fit residues: 165.6996 Evaluate side-chains 409 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 358 time to evaluate : 1.679 ------------------------------------------------------------------------------- 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 14 GLU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 82 ARG Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 107 CYS Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 107 CYS Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 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 100 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 96 optimal weight: 0.6980 chunk 48 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 102 optimal weight: 0.0980 chunk 110 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 15 optimal weight: 0.3980 chunk 127 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14161 Z= 0.149 Angle : 0.512 11.180 19390 Z= 0.259 Chirality : 0.037 0.154 2193 Planarity : 0.005 0.043 2455 Dihedral : 3.722 35.257 1863 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.89 % Allowed : 24.39 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (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: 2.51 (0.21), residues: 1695 helix: 2.10 (0.15), residues: 1221 sheet: None (None), residues: 0 loop : 0.64 (0.31), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 71 HIS 0.003 0.001 HIS E 47 PHE 0.011 0.001 PHE K 97 TYR 0.005 0.001 TYR K 88 ARG 0.006 0.000 ARG F 82 *********************** 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 405 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 362 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 76 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6694 (mp) REVERT: D 18 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8506 (t80) REVERT: E 29 ASP cc_start: 0.9007 (m-30) cc_final: 0.8622 (m-30) REVERT: G 22 ASP cc_start: 0.8685 (p0) cc_final: 0.8261 (p0) REVERT: G 71 TRP cc_start: 0.8276 (t60) cc_final: 0.7841 (t60) REVERT: G 77 GLU cc_start: 0.5907 (pm20) cc_final: 0.5702 (pm20) REVERT: G 82 ARG cc_start: 0.8130 (ttp-110) cc_final: 0.7482 (mtp85) REVERT: F 18 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8606 (t80) REVERT: F 64 GLU cc_start: 0.7704 (tp30) cc_final: 0.7365 (mt-10) REVERT: K 39 ARG cc_start: 0.8286 (ttm110) cc_final: 0.7969 (ttm-80) REVERT: K 75 ASN cc_start: 0.8454 (t0) cc_final: 0.8213 (t0) REVERT: J 84 LEU cc_start: 0.8229 (mt) cc_final: 0.7924 (mp) REVERT: J 96 LYS cc_start: 0.8734 (ptmt) cc_final: 0.8533 (ptmt) REVERT: L 29 ASP cc_start: 0.9032 (m-30) cc_final: 0.8629 (m-30) REVERT: L 91 THR cc_start: 0.8673 (m) cc_final: 0.8423 (m) outliers start: 43 outliers final: 27 residues processed: 389 average time/residue: 0.2701 time to fit residues: 151.4654 Evaluate side-chains 379 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 349 time to evaluate : 1.638 ------------------------------------------------------------------------------- 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 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 76 LEU Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain 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 I residue 13 VAL Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 74 VAL 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 155 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 150 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 99 optimal weight: 0.0270 chunk 159 optimal weight: 4.9990 overall best weight: 2.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 47 HIS J 90 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14161 Z= 0.204 Angle : 0.561 14.858 19390 Z= 0.279 Chirality : 0.039 0.161 2193 Planarity : 0.005 0.042 2455 Dihedral : 3.755 35.224 1863 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.62 % Allowed : 24.46 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.21), residues: 1695 helix: 2.19 (0.15), residues: 1193 sheet: None (None), residues: 0 loop : 0.51 (0.30), residues: 502 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 0.015 0.001 PHE K 97 TYR 0.010 0.001 TYR H 88 ARG 0.005 0.000 ARG F 82 *********************** 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 397 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 358 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 CYS cc_start: 0.8342 (m) cc_final: 0.7962 (t) REVERT: C 76 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6628 (mp) REVERT: D 18 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.8536 (t80) REVERT: G 22 ASP cc_start: 0.8694 (p0) cc_final: 0.8270 (p0) REVERT: F 16 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8557 (mp) REVERT: F 18 PHE cc_start: 0.9151 (OUTLIER) cc_final: 0.8615 (t80) REVERT: F 64 GLU cc_start: 0.7832 (tp30) cc_final: 0.7421 (mt-10) REVERT: F 96 LYS cc_start: 0.8874 (ptpt) cc_final: 0.8615 (ptmt) REVERT: K 75 ASN cc_start: 0.8442 (t0) cc_final: 0.8196 (t0) REVERT: J 22 ASP cc_start: 0.8627 (p0) cc_final: 0.8224 (p0) REVERT: J 84 LEU cc_start: 0.8238 (mt) cc_final: 0.7923 (mp) REVERT: L 91 THR cc_start: 0.8731 (m) cc_final: 0.8467 (m) outliers start: 39 outliers final: 32 residues processed: 383 average time/residue: 0.2623 time to fit residues: 143.9438 Evaluate side-chains 383 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 347 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 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 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 I residue 13 VAL Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 139 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 110 optimal weight: 0.0980 chunk 167 optimal weight: 0.5980 chunk 154 optimal weight: 5.9990 chunk 133 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 102 optimal weight: 0.0470 chunk 81 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 141 optimal weight: 5.9990 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 47 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14161 Z= 0.149 Angle : 0.538 14.002 19390 Z= 0.269 Chirality : 0.037 0.155 2193 Planarity : 0.005 0.042 2455 Dihedral : 3.672 34.776 1863 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.49 % Allowed : 24.59 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.21), residues: 1695 helix: 2.24 (0.15), residues: 1195 sheet: None (None), residues: 0 loop : 0.72 (0.30), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 71 HIS 0.002 0.000 HIS G 104 PHE 0.011 0.001 PHE K 97 TYR 0.014 0.001 TYR B 88 ARG 0.005 0.000 ARG F 82 ********************** 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 394 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 357 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 76 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6645 (mp) REVERT: D 18 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8566 (t80) REVERT: G 22 ASP cc_start: 0.8694 (p0) cc_final: 0.8262 (p0) REVERT: F 16 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8495 (mp) REVERT: F 18 PHE cc_start: 0.9116 (OUTLIER) cc_final: 0.8598 (t80) REVERT: F 64 GLU cc_start: 0.7866 (tp30) cc_final: 0.7463 (mt-10) REVERT: H 1 MET cc_start: 0.7361 (mtp) cc_final: 0.6918 (ttm) REVERT: K 75 ASN cc_start: 0.8385 (t0) cc_final: 0.8146 (t0) REVERT: L 4 ASP cc_start: 0.8496 (t0) cc_final: 0.8105 (t0) REVERT: L 91 THR cc_start: 0.8664 (m) cc_final: 0.8419 (m) outliers start: 37 outliers final: 26 residues processed: 380 average time/residue: 0.2674 time to fit residues: 145.8141 Evaluate side-chains 377 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 347 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain 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 D residue 18 PHE Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain 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 I residue 13 VAL Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 61 CYS 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 40 optimal weight: 0.0770 chunk 122 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 55 optimal weight: 0.0570 chunk 137 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 chunk 117 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 overall best weight: 0.9660 ------------------------------------------------------------------------------- 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 = 0.3160 r_free = 0.3160 target = 0.097640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.075309 restraints weight = 45212.441| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 2.60 r_work: 0.2551 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14161 Z= 0.156 Angle : 0.545 13.742 19390 Z= 0.269 Chirality : 0.038 0.159 2193 Planarity : 0.005 0.041 2455 Dihedral : 3.622 34.287 1863 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.56 % Allowed : 24.52 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.21), residues: 1695 helix: 2.27 (0.15), residues: 1186 sheet: None (None), residues: 0 loop : 0.79 (0.30), residues: 509 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 0.013 0.001 PHE K 97 TYR 0.016 0.001 TYR B 88 ARG 0.005 0.000 ARG F 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3453.17 seconds wall clock time: 63 minutes 20.35 seconds (3800.35 seconds total)