Starting phenix.real_space_refine on Mon Sep 14 17:12:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w6f_65686/09_2026/9w6f_65686.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w6f_65686/09_2026/9w6f_65686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w6f_65686/09_2026/9w6f_65686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w6f_65686/09_2026/9w6f_65686.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w6f_65686/09_2026/9w6f_65686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w6f_65686/09_2026/9w6f_65686.map" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians P 708 5.49 5 S 42 5.16 5 C 17863 2.51 5 N 5975 2.21 5 O 7298 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31886 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 744 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "D" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "G" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 776 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "H" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 679 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "I" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2433 Classifications: {'DNA': 118} Link IDs: {'rna3p': 117} Chain: "J" Number of atoms: 2405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2405 Classifications: {'DNA': 118} Link IDs: {'rna3p': 117} Chain: "K" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "L" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 698 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "M" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 767 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "N" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "O" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "P" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "Q" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 785 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "R" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 679 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "S" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2433 Classifications: {'DNA': 118} Link IDs: {'rna3p': 117} Chain: "T" Number of atoms: 2405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2405 Classifications: {'DNA': 118} Link IDs: {'rna3p': 117} Chain: "U" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "V" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "W" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 785 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "X" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "Y" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "Z" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 698 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "a" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 785 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "b" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 679 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "c" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2433 Classifications: {'DNA': 118} Link IDs: {'rna3p': 117} Chain: "d" Number of atoms: 2405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2405 Classifications: {'DNA': 118} Link IDs: {'rna3p': 117} Time building chain proxies: 6.44, per 1000 atoms: 0.20 Number of scatterers: 31886 At special positions: 0 Unit cell: (168.3, 161.7, 151.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 708 15.00 O 7298 8.00 N 5975 7.00 C 17863 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 2.76 Conformation dependent library (CDL) restraints added in 926.3 milliseconds 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4076 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 24 sheets defined 72.5% alpha, 2.6% beta 349 base pairs and 520 stacking pairs defined. Time for finding SS restraints: 4.41 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.585A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.704A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.722A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.958A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.537A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.552A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 4.316A pdb=" N GLY D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.525A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 121 removed outlier: 3.857A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.885A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.866A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.596A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.289A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.568A pdb=" N MET H 59 " --> pdb=" O SER H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 122 Processing helix chain 'K' and resid 44 through 57 Processing helix chain 'K' and resid 63 through 76 removed outlier: 3.582A pdb=" N PHE K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 114 Processing helix chain 'K' and resid 120 through 132 Processing helix chain 'L' and resid 25 through 29 removed outlier: 3.579A pdb=" N ILE L 29 " --> pdb=" O ILE L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 49 through 76 removed outlier: 3.899A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA L 76 " --> pdb=" O TYR L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 94 Processing helix chain 'M' and resid 26 through 36 Processing helix chain 'M' and resid 45 through 73 removed outlier: 4.362A pdb=" N VAL M 49 " --> pdb=" O ALA M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 90 Processing helix chain 'M' and resid 90 through 97 Processing helix chain 'N' and resid 37 through 49 Processing helix chain 'N' and resid 55 through 84 Processing helix chain 'N' and resid 90 through 102 removed outlier: 3.605A pdb=" N ILE N 94 " --> pdb=" O THR N 90 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 121 Processing helix chain 'O' and resid 44 through 55 Processing helix chain 'O' and resid 63 through 77 removed outlier: 4.052A pdb=" N ASP O 77 " --> pdb=" O GLU O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 120 through 132 Processing helix chain 'P' and resid 25 through 29 removed outlier: 3.957A pdb=" N ILE P 29 " --> pdb=" O ILE P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 42 Processing helix chain 'P' and resid 49 through 76 removed outlier: 3.812A pdb=" N GLU P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA P 76 " --> pdb=" O TYR P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 93 Processing helix chain 'Q' and resid 27 through 37 Processing helix chain 'Q' and resid 45 through 71 removed outlier: 4.419A pdb=" N VAL Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 90 Processing helix chain 'Q' and resid 90 through 97 Processing helix chain 'R' and resid 37 through 49 Processing helix chain 'R' and resid 55 through 84 Processing helix chain 'R' and resid 90 through 102 removed outlier: 3.707A pdb=" N ILE R 94 " --> pdb=" O THR R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 122 Processing helix chain 'U' and resid 44 through 55 Processing helix chain 'U' and resid 63 through 79 removed outlier: 3.958A pdb=" N ASP U 77 " --> pdb=" O GLU U 73 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE U 78 " --> pdb=" O ILE U 74 " (cutoff:3.500A) Processing helix chain 'U' and resid 85 through 114 Processing helix chain 'U' and resid 120 through 132 Processing helix chain 'V' and resid 25 through 29 Processing helix chain 'V' and resid 30 through 42 Processing helix chain 'V' and resid 50 through 76 Processing helix chain 'V' and resid 82 through 94 removed outlier: 3.583A pdb=" N VAL V 86 " --> pdb=" O THR V 82 " (cutoff:3.500A) Processing helix chain 'W' and resid 17 through 22 Processing helix chain 'W' and resid 27 through 38 removed outlier: 3.728A pdb=" N ASN W 38 " --> pdb=" O LEU W 34 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 73 removed outlier: 4.173A pdb=" N VAL W 49 " --> pdb=" O ALA W 45 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN W 73 " --> pdb=" O ALA W 69 " (cutoff:3.500A) Processing helix chain 'W' and resid 79 through 89 Processing helix chain 'W' and resid 90 through 97 Processing helix chain 'X' and resid 37 through 49 Processing helix chain 'X' and resid 55 through 84 Processing helix chain 'X' and resid 90 through 102 Processing helix chain 'X' and resid 104 through 121 removed outlier: 3.848A pdb=" N LYS X 108 " --> pdb=" O GLY X 104 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 55 Processing helix chain 'Y' and resid 63 through 77 removed outlier: 4.139A pdb=" N ASP Y 77 " --> pdb=" O GLU Y 73 " (cutoff:3.500A) Processing helix chain 'Y' and resid 85 through 114 Processing helix chain 'Y' and resid 120 through 132 Processing helix chain 'Z' and resid 25 through 29 Processing helix chain 'Z' and resid 30 through 41 Processing helix chain 'Z' and resid 49 through 76 removed outlier: 3.836A pdb=" N GLU Z 53 " --> pdb=" O LEU Z 49 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP Z 68 " --> pdb=" O ASN Z 64 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR Z 71 " --> pdb=" O ARG Z 67 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA Z 76 " --> pdb=" O TYR Z 72 " (cutoff:3.500A) Processing helix chain 'Z' and resid 82 through 92 removed outlier: 3.601A pdb=" N VAL Z 86 " --> pdb=" O THR Z 82 " (cutoff:3.500A) Processing helix chain 'a' and resid 17 through 21 Processing helix chain 'a' and resid 26 through 37 Processing helix chain 'a' and resid 45 through 73 removed outlier: 4.486A pdb=" N VAL a 49 " --> pdb=" O ALA a 45 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN a 73 " --> pdb=" O ALA a 69 " (cutoff:3.500A) Processing helix chain 'a' and resid 79 through 88 Processing helix chain 'a' and resid 90 through 97 Processing helix chain 'b' and resid 37 through 49 Processing helix chain 'b' and resid 56 through 84 Processing helix chain 'b' and resid 90 through 102 removed outlier: 3.607A pdb=" N ILE b 94 " --> pdb=" O THR b 90 " (cutoff:3.500A) Processing helix chain 'b' and resid 104 through 122 removed outlier: 3.832A pdb=" N LYS b 108 " --> pdb=" O GLY b 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.620A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.685A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.273A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.201A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.428A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'K' and resid 118 through 119 Processing sheet with id=AB1, first strand: chain 'L' and resid 96 through 98 removed outlier: 6.611A pdb=" N THR L 96 " --> pdb=" O THR Q 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'M' and resid 42 through 43 removed outlier: 8.205A pdb=" N ARG M 42 " --> pdb=" O ILE N 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'M' and resid 101 through 102 removed outlier: 6.904A pdb=" N THR M 101 " --> pdb=" O TYR P 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'O' and resid 83 through 84 removed outlier: 6.859A pdb=" N ARG O 83 " --> pdb=" O VAL P 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'O' and resid 118 through 119 Processing sheet with id=AB6, first strand: chain 'Q' and resid 42 through 43 removed outlier: 7.647A pdb=" N ARG Q 42 " --> pdb=" O ILE R 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'Q' and resid 77 through 78 Processing sheet with id=AB8, first strand: chain 'U' and resid 83 through 84 removed outlier: 7.034A pdb=" N ARG U 83 " --> pdb=" O VAL V 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'U' and resid 118 through 119 removed outlier: 3.557A pdb=" N ILE U 119 " --> pdb=" O ARG V 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'V' and resid 96 through 98 removed outlier: 6.840A pdb=" N THR V 96 " --> pdb=" O THR a 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'W' and resid 42 through 43 removed outlier: 7.318A pdb=" N ARG W 42 " --> pdb=" O ILE X 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'W' and resid 77 through 78 Processing sheet with id=AC4, first strand: chain 'W' and resid 101 through 102 removed outlier: 6.770A pdb=" N THR W 101 " --> pdb=" O TYR Z 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'Y' and resid 83 through 84 removed outlier: 7.313A pdb=" N ARG Y 83 " --> pdb=" O VAL Z 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'Y' and resid 118 through 119 1152 hydrogen bonds defined for protein. 3414 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 905 hydrogen bonds 1806 hydrogen bond angles 0 basepair planarities 349 basepair parallelities 520 stacking parallelities Total time for adding SS restraints: 6.72 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5156 1.33 - 1.45: 11340 1.45 - 1.57: 15915 1.57 - 1.69: 1410 1.69 - 1.81: 72 Bond restraints: 33893 Sorted by residual: bond pdb=" C1' DT d 38 " pdb=" N1 DT d 38 " ideal model delta sigma weight residual 1.468 1.540 -0.072 1.40e-02 5.10e+03 2.61e+01 bond pdb=" C3' DG c -37 " pdb=" C2' DG c -37 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.28e+01 bond pdb=" C3' DA c 43 " pdb=" C2' DA c 43 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.18e+01 bond pdb=" C3' DG T -49 " pdb=" C2' DG T -49 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" C3' DC T -8 " pdb=" C2' DC T -8 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 ... (remaining 33888 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 43982 1.02 - 2.04: 3480 2.04 - 3.05: 1289 3.05 - 4.07: 32 4.07 - 5.09: 18 Bond angle restraints: 48801 Sorted by residual: angle pdb=" O4' DA d 39 " pdb=" C4' DA d 39 " pdb=" C3' DA d 39 " ideal model delta sigma weight residual 106.00 102.99 3.01 6.00e-01 2.78e+00 2.52e+01 angle pdb=" O4' DA c -45 " pdb=" C4' DA c -45 " pdb=" C3' DA c -45 " ideal model delta sigma weight residual 106.00 103.24 2.76 6.00e-01 2.78e+00 2.12e+01 angle pdb=" N3 DT I 66 " pdb=" C4 DT I 66 " pdb=" O4 DT I 66 " ideal model delta sigma weight residual 119.90 122.61 -2.71 6.00e-01 2.78e+00 2.04e+01 angle pdb=" O4' DA S 47 " pdb=" C4' DA S 47 " pdb=" C3' DA S 47 " ideal model delta sigma weight residual 106.00 103.29 2.71 6.00e-01 2.78e+00 2.04e+01 angle pdb=" N3 DT I 31 " pdb=" C4 DT I 31 " pdb=" O4 DT I 31 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 ... (remaining 48796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 13571 17.93 - 35.86: 2219 35.86 - 53.79: 2162 53.79 - 71.72: 545 71.72 - 89.66: 41 Dihedral angle restraints: 18538 sinusoidal: 12209 harmonic: 6329 Sorted by residual: dihedral pdb=" CA PRO N 103 " pdb=" C PRO N 103 " pdb=" N GLY N 104 " pdb=" CA GLY N 104 " ideal model delta harmonic sigma weight residual 180.00 -164.46 -15.54 0 5.00e+00 4.00e-02 9.66e+00 dihedral pdb=" CA ARG C 29 " pdb=" CB ARG C 29 " pdb=" CG ARG C 29 " pdb=" CD ARG C 29 " ideal model delta sinusoidal sigma weight residual -60.00 -116.48 56.48 3 1.50e+01 4.44e-03 9.40e+00 dihedral pdb=" CA ARG D 79 " pdb=" CB ARG D 79 " pdb=" CG ARG D 79 " pdb=" CD ARG D 79 " ideal model delta sinusoidal sigma weight residual -180.00 -123.74 -56.26 3 1.50e+01 4.44e-03 9.39e+00 ... (remaining 18535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 3123 0.030 - 0.060: 1667 0.060 - 0.090: 549 0.090 - 0.121: 221 0.121 - 0.151: 6 Chirality restraints: 5566 Sorted by residual: chirality pdb=" C1' DT d 38 " pdb=" O4' DT d 38 " pdb=" C2' DT d 38 " pdb=" N1 DT d 38 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CA ILE W 79 " pdb=" N ILE W 79 " pdb=" C ILE W 79 " pdb=" CB ILE W 79 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA ILE Q 79 " pdb=" N ILE Q 79 " pdb=" C ILE Q 79 " pdb=" CB ILE Q 79 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 5563 not shown) Planarity restraints: 3717 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE W 79 " -0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO W 80 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO W 80 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO W 80 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE Q 79 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.63e+00 pdb=" N PRO Q 80 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO Q 80 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO Q 80 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 62 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.43e+00 pdb=" C LEU F 62 " -0.027 2.00e-02 2.50e+03 pdb=" O LEU F 62 " 0.010 2.00e-02 2.50e+03 pdb=" N GLU F 63 " 0.009 2.00e-02 2.50e+03 ... (remaining 3714 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2112 2.74 - 3.28: 28874 3.28 - 3.82: 60482 3.82 - 4.36: 67346 4.36 - 4.90: 102164 Nonbonded interactions: 260978 Sorted by model distance: nonbonded pdb=" OD1 ASP L 85 " pdb=" OH TYR N 83 " model vdw 2.196 3.040 nonbonded pdb=" OH TYR Y 99 " pdb=" OE1 GLU Y 133 " model vdw 2.255 3.040 nonbonded pdb=" N3 DT d 38 " pdb=" N7 DA d 39 " model vdw 2.258 3.200 nonbonded pdb=" O VAL N 48 " pdb=" NH2 ARG Z 17 " model vdw 2.282 3.120 nonbonded pdb=" NH2 ARG F 35 " pdb=" OP2 DG I 8 " model vdw 2.304 3.120 ... (remaining 260973 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' selection = chain 'E' selection = chain 'K' selection = chain 'O' selection = chain 'U' selection = chain 'Y' } ncs_group { reference = (chain 'B' and resid 25 through 100) selection = chain 'F' selection = (chain 'L' and resid 25 through 100) selection = (chain 'P' and resid 25 through 100) selection = (chain 'V' and resid 25 through 100) selection = (chain 'Z' and resid 25 through 100) } ncs_group { reference = (chain 'C' and resid 23 through 117) selection = (chain 'G' and resid 23 through 117) selection = (chain 'M' and resid 23 through 117) selection = (chain 'Q' and resid 23 through 117) selection = (chain 'W' and resid 23 through 117) selection = (chain 'a' and resid 23 through 117) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 36 through 121) selection = chain 'N' selection = (chain 'R' and resid 36 through 121) selection = chain 'X' selection = (chain 'b' and resid 36 through 121) } ncs_group { reference = chain 'I' selection = chain 'S' selection = chain 'c' } ncs_group { reference = chain 'J' selection = chain 'T' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 30.920 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 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 : 0.005 0.072 33893 Z= 0.479 Angle : 0.634 5.091 48801 Z= 0.599 Chirality : 0.041 0.151 5566 Planarity : 0.003 0.045 3717 Dihedral : 24.423 89.655 14462 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.38 (0.19), residues: 2139 helix: 3.30 (0.13), residues: 1510 sheet: None (None), residues: 0 loop : -0.56 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 53 TYR 0.008 0.001 TYR b 40 PHE 0.005 0.001 PHE H 65 HIS 0.003 0.000 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.48 (33893) covalent geometry : angle 0.63403 / 0.60 (48801) hydrogen bonds : bond 0.10028 / 7.00 ( 2057) hydrogen bonds : angle 2.99808 / 2.18 ( 5220) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 536 time to evaluate : 0.882 Fit side-chains REVERT: A 78 PHE cc_start: 0.6144 (m-80) cc_final: 0.5941 (m-10) REVERT: B 67 ARG cc_start: 0.7599 (ttm110) cc_final: 0.7358 (ttm110) REVERT: B 70 VAL cc_start: 0.7948 (t) cc_final: 0.7348 (m) REVERT: B 77 LYS cc_start: 0.7963 (mtmm) cc_final: 0.7683 (mttp) REVERT: C 68 ASN cc_start: 0.7186 (t0) cc_final: 0.6825 (m110) REVERT: D 43 LYS cc_start: 0.7018 (mmmt) cc_final: 0.6309 (mmtt) REVERT: D 52 THR cc_start: 0.7018 (m) cc_final: 0.6376 (t) REVERT: D 92 ARG cc_start: 0.6395 (mtp85) cc_final: 0.6183 (mtp85) REVERT: E 42 ARG cc_start: 0.7273 (mmm-85) cc_final: 0.6995 (mmm-85) REVERT: F 84 MET cc_start: 0.7120 (tpt) cc_final: 0.6812 (tpt) REVERT: F 88 TYR cc_start: 0.7517 (m-10) cc_final: 0.6022 (m-10) REVERT: F 93 GLN cc_start: 0.7823 (mt0) cc_final: 0.7593 (mt0) REVERT: H 51 ASP cc_start: 0.6798 (p0) cc_final: 0.5887 (t70) REVERT: H 70 PHE cc_start: 0.8465 (t80) cc_final: 0.8247 (t80) REVERT: H 83 TYR cc_start: 0.6189 (m-10) cc_final: 0.5632 (m-10) REVERT: H 86 ARG cc_start: 0.6939 (mtp85) cc_final: 0.6704 (mtp85) REVERT: L 49 LEU cc_start: 0.7570 (mm) cc_final: 0.7370 (mm) REVERT: M 35 ARG cc_start: 0.6527 (ttp80) cc_final: 0.6225 (mtp180) REVERT: M 49 VAL cc_start: 0.7523 (t) cc_final: 0.7203 (p) REVERT: N 46 LYS cc_start: 0.5996 (tttt) cc_final: 0.4999 (mtpt) REVERT: N 62 MET cc_start: 0.7841 (mmm) cc_final: 0.7587 (mmm) REVERT: N 83 TYR cc_start: 0.5314 (t80) cc_final: 0.5054 (t80) REVERT: P 82 THR cc_start: 0.6565 (t) cc_final: 0.6278 (t) REVERT: Q 110 ASN cc_start: 0.7188 (t0) cc_final: 0.6779 (t0) REVERT: R 76 GLU cc_start: 0.7435 (tp30) cc_final: 0.6958 (tp30) REVERT: R 85 LYS cc_start: 0.7080 (mttt) cc_final: 0.6384 (mmtt) REVERT: R 111 VAL cc_start: 0.8199 (t) cc_final: 0.7996 (t) REVERT: U 73 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7345 (tm-30) REVERT: U 90 MET cc_start: 0.7181 (mmm) cc_final: 0.6822 (mmp) REVERT: V 35 ARG cc_start: 0.7947 (mmm160) cc_final: 0.7666 (mmm-85) REVERT: V 36 ARG cc_start: 0.8174 (mtm-85) cc_final: 0.7892 (mtm180) REVERT: W 74 LYS cc_start: 0.6313 (mttt) cc_final: 0.5949 (tmtt) REVERT: W 104 GLN cc_start: 0.7220 (mt0) cc_final: 0.6950 (mt0) REVERT: X 42 TYR cc_start: 0.7123 (t80) cc_final: 0.6759 (t80) REVERT: X 68 ASP cc_start: 0.7923 (t70) cc_final: 0.7628 (t0) REVERT: Y 79 LYS cc_start: 0.6592 (tttt) cc_final: 0.6157 (tptt) REVERT: Z 29 ILE cc_start: 0.8123 (mm) cc_final: 0.7786 (tt) REVERT: Z 88 TYR cc_start: 0.7072 (m-10) cc_final: 0.6515 (m-10) REVERT: a 99 LYS cc_start: 0.7256 (mmtp) cc_final: 0.7005 (mmtp) REVERT: a 104 GLN cc_start: 0.7156 (mt0) cc_final: 0.6719 (mm-40) REVERT: b 43 LYS cc_start: 0.6882 (mttt) cc_final: 0.6362 (mtpp) REVERT: b 85 LYS cc_start: 0.7268 (mttt) cc_final: 0.6937 (mttm) outliers start: 0 outliers final: 0 residues processed: 536 average time/residue: 0.2859 time to fit residues: 221.3269 Evaluate side-chains 307 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS G 68 ASN H 95 GLN K 55 GLN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 ASN L 27 GLN O 85 GLN U 85 GLN X 63 ASN Y 39 HIS Y 68 GLN Y 93 GLN Z 18 HIS b 95 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.143963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.108846 restraints weight = 62249.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.108737 restraints weight = 71564.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.109381 restraints weight = 65328.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.109526 restraints weight = 55734.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.109730 restraints weight = 54287.779| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 33893 Z= 0.247 Angle : 0.762 10.341 48801 Z= 0.427 Chirality : 0.050 0.381 5566 Planarity : 0.007 0.072 3717 Dihedral : 29.310 89.294 10137 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.23 % Allowed : 9.62 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.18), residues: 2139 helix: 2.10 (0.13), residues: 1516 sheet: None (None), residues: 0 loop : -1.24 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 17 TYR 0.026 0.003 TYR D 121 PHE 0.025 0.003 PHE O 78 HIS 0.014 0.003 HIS N 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.25 (33893) covalent geometry : angle 0.76222 / 0.43 (48801) hydrogen bonds : bond 0.07658 / 5.16 ( 2057) hydrogen bonds : angle 3.23634 / 2.34 ( 5220) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 305 time to evaluate : 0.907 Fit side-chains REVERT: A 94 GLU cc_start: 0.6780 (mm-30) cc_final: 0.6463 (mm-30) REVERT: B 67 ARG cc_start: 0.7710 (ttm110) cc_final: 0.7482 (ttp80) REVERT: B 77 LYS cc_start: 0.8063 (mtmm) cc_final: 0.7849 (mtmm) REVERT: C 68 ASN cc_start: 0.7553 (t0) cc_final: 0.6933 (m-40) REVERT: D 43 LYS cc_start: 0.6991 (mmmt) cc_final: 0.6250 (mmtt) REVERT: D 52 THR cc_start: 0.6883 (m) cc_final: 0.6257 (t) REVERT: D 61 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8002 (mp) REVERT: F 84 MET cc_start: 0.7469 (tpt) cc_final: 0.7225 (tpt) REVERT: F 93 GLN cc_start: 0.8088 (mt0) cc_final: 0.7814 (mt0) REVERT: G 112 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7770 (mm-40) REVERT: H 47 GLN cc_start: 0.7464 (tt0) cc_final: 0.7236 (tt0) REVERT: H 51 ASP cc_start: 0.6369 (p0) cc_final: 0.6095 (t70) REVERT: N 46 LYS cc_start: 0.5934 (tttt) cc_final: 0.5314 (mtpt) REVERT: N 99 ARG cc_start: 0.7919 (mtp85) cc_final: 0.7589 (mtp-110) REVERT: R 76 GLU cc_start: 0.7297 (tp30) cc_final: 0.7042 (tp30) REVERT: R 85 LYS cc_start: 0.7131 (mttt) cc_final: 0.6702 (mmtt) REVERT: U 106 ASP cc_start: 0.6791 (m-30) cc_final: 0.6584 (m-30) REVERT: V 68 ASP cc_start: 0.7648 (m-30) cc_final: 0.7259 (m-30) REVERT: W 95 LYS cc_start: 0.8096 (tttp) cc_final: 0.7751 (tttp) REVERT: X 42 TYR cc_start: 0.7161 (t80) cc_final: 0.6770 (t80) REVERT: Y 79 LYS cc_start: 0.6691 (tttt) cc_final: 0.6364 (tptt) REVERT: Z 84 MET cc_start: 0.6786 (tpp) cc_final: 0.6520 (tpp) REVERT: Z 88 TYR cc_start: 0.7385 (m-10) cc_final: 0.6709 (m-10) REVERT: a 63 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8066 (mt) REVERT: b 43 LYS cc_start: 0.7004 (mttt) cc_final: 0.6598 (mtpp) REVERT: b 62 MET cc_start: 0.8149 (mmm) cc_final: 0.7904 (tpt) outliers start: 59 outliers final: 40 residues processed: 348 average time/residue: 0.2390 time to fit residues: 127.1878 Evaluate side-chains 309 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 267 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain O residue 62 ILE Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain W residue 101 THR Chi-restraints excluded: chain X residue 52 THR Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 112 SER Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 73 THR Chi-restraints excluded: chain Z residue 82 THR Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 63 LEU Chi-restraints excluded: chain a residue 75 LYS Chi-restraints excluded: chain b residue 115 THR Chi-restraints excluded: chain b residue 119 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 264 optimal weight: 50.0000 chunk 114 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 89 optimal weight: 50.0000 chunk 210 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 226 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN L 25 ASN M 68 ASN N 84 ASN ** Q 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 108 ASN a 110 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.144098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.108788 restraints weight = 62276.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.108957 restraints weight = 69560.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.109370 restraints weight = 68670.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.109591 restraints weight = 57894.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.109788 restraints weight = 55747.111| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 33893 Z= 0.173 Angle : 0.586 9.307 48801 Z= 0.353 Chirality : 0.042 0.323 5566 Planarity : 0.005 0.048 3717 Dihedral : 29.234 88.461 10137 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.12 % Allowed : 11.26 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.18), residues: 2139 helix: 2.57 (0.13), residues: 1516 sheet: None (None), residues: 0 loop : -1.28 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 131 TYR 0.031 0.002 TYR F 88 PHE 0.012 0.002 PHE O 78 HIS 0.010 0.001 HIS N 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.17 (33893) covalent geometry : angle 0.58593 / 0.35 (48801) hydrogen bonds : bond 0.05899 / 3.96 ( 2057) hydrogen bonds : angle 2.94600 / 2.14 ( 5220) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 286 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.6629 (mm-30) cc_final: 0.6316 (mm-30) REVERT: C 32 ARG cc_start: 0.6157 (OUTLIER) cc_final: 0.5703 (ptt180) REVERT: C 68 ASN cc_start: 0.7361 (t0) cc_final: 0.7077 (m-40) REVERT: D 52 THR cc_start: 0.6793 (m) cc_final: 0.6265 (t) REVERT: F 93 GLN cc_start: 0.8042 (mt0) cc_final: 0.7740 (mt0) REVERT: G 68 ASN cc_start: 0.6742 (m-40) cc_final: 0.6490 (m110) REVERT: G 118 LYS cc_start: 0.4062 (OUTLIER) cc_final: 0.2902 (ttpt) REVERT: H 51 ASP cc_start: 0.6400 (p0) cc_final: 0.6033 (t70) REVERT: N 46 LYS cc_start: 0.5920 (tttt) cc_final: 0.5225 (mtpt) REVERT: N 99 ARG cc_start: 0.7938 (mtp85) cc_final: 0.7586 (mtp-110) REVERT: R 76 GLU cc_start: 0.7546 (tp30) cc_final: 0.7302 (tp30) REVERT: R 85 LYS cc_start: 0.7077 (mttt) cc_final: 0.6677 (mmtt) REVERT: W 95 LYS cc_start: 0.8038 (tttp) cc_final: 0.7724 (tttp) REVERT: X 42 TYR cc_start: 0.7050 (t80) cc_final: 0.6675 (t80) REVERT: Y 79 LYS cc_start: 0.6710 (tttt) cc_final: 0.6292 (tptt) REVERT: Z 88 TYR cc_start: 0.7182 (m-10) cc_final: 0.6932 (m-10) REVERT: a 42 ARG cc_start: 0.6922 (mtp85) cc_final: 0.6636 (mtp85) REVERT: a 63 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7938 (mt) REVERT: b 43 LYS cc_start: 0.7088 (mttt) cc_final: 0.6628 (mtpp) REVERT: b 62 MET cc_start: 0.8128 (mmm) cc_final: 0.7734 (tpt) outliers start: 57 outliers final: 39 residues processed: 326 average time/residue: 0.2417 time to fit residues: 120.5645 Evaluate side-chains 315 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 273 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain C residue 32 ARG Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain O residue 62 ILE Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain W residue 56 GLU Chi-restraints excluded: chain W residue 101 THR Chi-restraints excluded: chain X residue 52 THR Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 101 LEU Chi-restraints excluded: chain X residue 112 SER Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 73 THR Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 63 LEU Chi-restraints excluded: chain a residue 75 LYS Chi-restraints excluded: chain b residue 54 ILE Chi-restraints excluded: chain b residue 90 THR Chi-restraints excluded: chain b residue 94 ILE Chi-restraints excluded: chain b residue 119 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 248 optimal weight: 5.9990 chunk 235 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 167 optimal weight: 50.0000 chunk 263 optimal weight: 50.0000 chunk 247 optimal weight: 2.9990 chunk 228 optimal weight: 3.9990 chunk 201 optimal weight: 8.9990 chunk 145 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN E 113 HIS ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 68 ASN O 85 GLN ** Q 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.141914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.105966 restraints weight = 61710.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.106115 restraints weight = 70224.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.106474 restraints weight = 66024.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.106708 restraints weight = 57830.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.106862 restraints weight = 55506.368| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 33893 Z= 0.196 Angle : 0.653 7.886 48801 Z= 0.379 Chirality : 0.045 0.358 5566 Planarity : 0.006 0.056 3717 Dihedral : 29.431 89.940 10137 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.94 % Allowed : 12.68 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.18), residues: 2139 helix: 2.28 (0.13), residues: 1515 sheet: None (None), residues: 0 loop : -1.44 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 128 TYR 0.027 0.002 TYR F 88 PHE 0.015 0.002 PHE O 78 HIS 0.007 0.002 HIS Z 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.20 (33893) covalent geometry : angle 0.65295 / 0.38 (48801) hydrogen bonds : bond 0.06682 / 4.48 ( 2057) hydrogen bonds : angle 3.10776 / 2.26 ( 5220) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 276 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.6721 (mm-30) cc_final: 0.6402 (mm-30) REVERT: C 29 ARG cc_start: 0.6892 (OUTLIER) cc_final: 0.6509 (ttp80) REVERT: C 32 ARG cc_start: 0.6180 (OUTLIER) cc_final: 0.5577 (ptt180) REVERT: C 35 ARG cc_start: 0.7369 (mmt180) cc_final: 0.7139 (mmm-85) REVERT: D 61 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.7959 (mp) REVERT: H 51 ASP cc_start: 0.6385 (p0) cc_final: 0.6094 (t70) REVERT: K 133 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6241 (mp0) REVERT: N 46 LYS cc_start: 0.6092 (tttt) cc_final: 0.5371 (mtpt) REVERT: N 59 MET cc_start: 0.7441 (mmm) cc_final: 0.7229 (mmm) REVERT: N 80 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8020 (mm) REVERT: N 99 ARG cc_start: 0.7836 (mtp85) cc_final: 0.7504 (mtp-110) REVERT: Q 56 GLU cc_start: 0.7509 (tt0) cc_final: 0.7292 (tp30) REVERT: R 39 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7745 (tp) REVERT: R 76 GLU cc_start: 0.7463 (tp30) cc_final: 0.7164 (tp30) REVERT: R 85 LYS cc_start: 0.7089 (mttt) cc_final: 0.6782 (mmtt) REVERT: U 64 LYS cc_start: 0.7759 (mttm) cc_final: 0.7396 (mtpp) REVERT: V 85 ASP cc_start: 0.7924 (m-30) cc_final: 0.7614 (m-30) REVERT: W 95 LYS cc_start: 0.8029 (tttp) cc_final: 0.7724 (tttp) REVERT: X 42 TYR cc_start: 0.7074 (t80) cc_final: 0.6668 (t80) REVERT: Y 79 LYS cc_start: 0.6705 (tttt) cc_final: 0.6240 (tptt) REVERT: a 42 ARG cc_start: 0.6978 (mtp85) cc_final: 0.6580 (mtp85) REVERT: a 63 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8064 (mt) REVERT: b 43 LYS cc_start: 0.7054 (mttt) cc_final: 0.6560 (mtpp) outliers start: 72 outliers final: 55 residues processed: 329 average time/residue: 0.2314 time to fit residues: 117.2095 Evaluate side-chains 325 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 263 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 32 ARG Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 133 GLU Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain O residue 62 ILE Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain V residue 80 THR Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain W residue 101 THR Chi-restraints excluded: chain X residue 52 THR Chi-restraints excluded: chain X residue 57 LYS Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 101 LEU Chi-restraints excluded: chain X residue 112 SER Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 73 THR Chi-restraints excluded: chain Z residue 82 THR Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 63 LEU Chi-restraints excluded: chain a residue 75 LYS Chi-restraints excluded: chain b residue 54 ILE Chi-restraints excluded: chain b residue 90 THR Chi-restraints excluded: chain b residue 94 ILE Chi-restraints excluded: chain b residue 115 THR Chi-restraints excluded: chain b residue 119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 16 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 chunk 179 optimal weight: 50.0000 chunk 41 optimal weight: 3.9990 chunk 79 optimal weight: 50.0000 chunk 248 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 76 optimal weight: 50.0000 chunk 189 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN G 112 GLN H 49 HIS L 25 ASN O 125 GLN Q 24 GLN a 110 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.143715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.108511 restraints weight = 62145.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.108577 restraints weight = 67575.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.108856 restraints weight = 68850.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.109077 restraints weight = 58751.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.109289 restraints weight = 56812.617| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 33893 Z= 0.140 Angle : 0.548 8.064 48801 Z= 0.336 Chirality : 0.040 0.315 5566 Planarity : 0.004 0.047 3717 Dihedral : 29.271 89.569 10137 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.57 % Allowed : 14.60 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.18), residues: 2139 helix: 2.74 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -1.39 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 83 TYR 0.038 0.001 TYR F 88 PHE 0.008 0.001 PHE D 65 HIS 0.005 0.001 HIS a 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.14 (33893) covalent geometry : angle 0.54841 / 0.34 (48801) hydrogen bonds : bond 0.05226 / 3.50 ( 2057) hydrogen bonds : angle 2.83341 / 2.06 ( 5220) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 282 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.6542 (mm-30) cc_final: 0.6273 (mm-30) REVERT: C 32 ARG cc_start: 0.6106 (OUTLIER) cc_final: 0.5564 (ptt180) REVERT: G 56 GLU cc_start: 0.6350 (mt-10) cc_final: 0.6050 (mm-30) REVERT: G 118 LYS cc_start: 0.4005 (OUTLIER) cc_final: 0.2905 (ttpt) REVERT: H 51 ASP cc_start: 0.6418 (p0) cc_final: 0.6061 (t70) REVERT: N 46 LYS cc_start: 0.5946 (tttt) cc_final: 0.5328 (mtpt) REVERT: N 99 ARG cc_start: 0.7794 (mtp85) cc_final: 0.7476 (mtp-110) REVERT: R 39 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7768 (tp) REVERT: R 76 GLU cc_start: 0.7472 (tp30) cc_final: 0.7173 (tp30) REVERT: R 85 LYS cc_start: 0.7084 (mttt) cc_final: 0.6761 (mmtt) REVERT: R 88 THR cc_start: 0.7102 (m) cc_final: 0.6716 (p) REVERT: U 64 LYS cc_start: 0.7562 (mttm) cc_final: 0.7224 (mtpp) REVERT: W 95 LYS cc_start: 0.8022 (tttp) cc_final: 0.7711 (tttp) REVERT: X 42 TYR cc_start: 0.7020 (t80) cc_final: 0.6693 (t80) REVERT: Y 79 LYS cc_start: 0.6516 (tttt) cc_final: 0.6087 (tptt) REVERT: a 42 ARG cc_start: 0.7002 (mtp85) cc_final: 0.6663 (mtp85) REVERT: a 63 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7946 (mt) REVERT: b 43 LYS cc_start: 0.7035 (mttt) cc_final: 0.6545 (mtpp) REVERT: b 59 MET cc_start: 0.6929 (tpp) cc_final: 0.6011 (mmm) REVERT: b 83 TYR cc_start: 0.6755 (t80) cc_final: 0.6555 (t80) outliers start: 47 outliers final: 35 residues processed: 317 average time/residue: 0.2293 time to fit residues: 112.6355 Evaluate side-chains 310 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 271 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain C residue 32 ARG Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain O residue 62 ILE Chi-restraints excluded: chain O residue 125 GLN Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain W residue 101 THR Chi-restraints excluded: chain X residue 52 THR Chi-restraints excluded: chain X residue 101 LEU Chi-restraints excluded: chain X residue 112 SER Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 73 THR Chi-restraints excluded: chain Z residue 82 THR Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 63 LEU Chi-restraints excluded: chain a residue 75 LYS Chi-restraints excluded: chain b residue 54 ILE Chi-restraints excluded: chain b residue 94 ILE Chi-restraints excluded: chain b residue 119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 255 optimal weight: 30.0000 chunk 166 optimal weight: 50.0000 chunk 51 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 170 optimal weight: 50.0000 chunk 92 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 200 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 107 optimal weight: 0.0010 overall best weight: 3.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 ASN O 125 GLN Q 24 GLN a 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.142587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.107229 restraints weight = 61763.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.107283 restraints weight = 73509.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.107799 restraints weight = 66679.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.107963 restraints weight = 58496.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.108147 restraints weight = 56525.368| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33893 Z= 0.165 Angle : 0.587 10.307 48801 Z= 0.350 Chirality : 0.042 0.328 5566 Planarity : 0.005 0.070 3717 Dihedral : 29.353 89.695 10137 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.39 % Allowed : 14.54 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.18), residues: 2139 helix: 2.63 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -1.42 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG Z 78 TYR 0.058 0.002 TYR F 88 PHE 0.012 0.002 PHE A 67 HIS 0.005 0.001 HIS N 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 (33893) covalent geometry : angle 0.58741 / 0.35 (48801) hydrogen bonds : bond 0.05661 / 3.79 ( 2057) hydrogen bonds : angle 2.93567 / 2.13 ( 5220) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 275 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.6637 (mm-30) cc_final: 0.6348 (mm-30) REVERT: C 32 ARG cc_start: 0.6095 (OUTLIER) cc_final: 0.5642 (ptt180) REVERT: D 61 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7879 (mp) REVERT: G 56 GLU cc_start: 0.6546 (mt-10) cc_final: 0.6177 (mm-30) REVERT: G 118 LYS cc_start: 0.3989 (OUTLIER) cc_final: 0.3033 (mmtp) REVERT: H 51 ASP cc_start: 0.6571 (p0) cc_final: 0.6152 (t70) REVERT: K 133 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6183 (mp0) REVERT: N 46 LYS cc_start: 0.5961 (tttt) cc_final: 0.5339 (mtpt) REVERT: N 99 ARG cc_start: 0.7803 (mtp85) cc_final: 0.7523 (mtp-110) REVERT: R 39 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7806 (tp) REVERT: R 76 GLU cc_start: 0.7442 (tp30) cc_final: 0.7155 (tp30) REVERT: R 85 LYS cc_start: 0.7090 (mttt) cc_final: 0.6750 (mmtt) REVERT: R 88 THR cc_start: 0.7103 (m) cc_final: 0.6698 (p) REVERT: U 64 LYS cc_start: 0.7646 (mttm) cc_final: 0.7297 (mtpp) REVERT: V 85 ASP cc_start: 0.7925 (m-30) cc_final: 0.7654 (m-30) REVERT: W 95 LYS cc_start: 0.8026 (tttp) cc_final: 0.7717 (tttp) REVERT: X 42 TYR cc_start: 0.7082 (t80) cc_final: 0.6730 (t80) REVERT: Y 79 LYS cc_start: 0.6463 (tttt) cc_final: 0.5955 (tptt) REVERT: a 42 ARG cc_start: 0.6967 (mtp85) cc_final: 0.6562 (mtp85) REVERT: a 63 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7996 (mt) REVERT: b 43 LYS cc_start: 0.7050 (mttt) cc_final: 0.6560 (mtpp) outliers start: 62 outliers final: 50 residues processed: 319 average time/residue: 0.2243 time to fit residues: 111.3656 Evaluate side-chains 326 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 270 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain C residue 32 ARG Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 133 GLU Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 92 ARG Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain O residue 62 ILE Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain W residue 101 THR Chi-restraints excluded: chain X residue 52 THR Chi-restraints excluded: chain X residue 57 LYS Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 101 LEU Chi-restraints excluded: chain X residue 112 SER Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 70 VAL Chi-restraints excluded: chain Z residue 73 THR Chi-restraints excluded: chain Z residue 82 THR Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 63 LEU Chi-restraints excluded: chain a residue 75 LYS Chi-restraints excluded: chain b residue 51 ASP Chi-restraints excluded: chain b residue 54 ILE Chi-restraints excluded: chain b residue 94 ILE Chi-restraints excluded: chain b residue 119 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 191 optimal weight: 5.9990 chunk 245 optimal weight: 0.7980 chunk 221 optimal weight: 8.9990 chunk 86 optimal weight: 40.0000 chunk 206 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 84 optimal weight: 50.0000 chunk 268 optimal weight: 40.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** Q 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.140944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.105254 restraints weight = 61726.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.105488 restraints weight = 68357.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.105891 restraints weight = 63207.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.106097 restraints weight = 57467.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.106258 restraints weight = 55653.142| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 33893 Z= 0.194 Angle : 0.649 8.224 48801 Z= 0.378 Chirality : 0.045 0.339 5566 Planarity : 0.005 0.047 3717 Dihedral : 29.512 89.928 10137 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.32 % Allowed : 14.05 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.18), residues: 2139 helix: 2.28 (0.13), residues: 1518 sheet: None (None), residues: 0 loop : -1.50 (0.23), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Z 78 TYR 0.067 0.002 TYR F 88 PHE 0.013 0.002 PHE A 67 HIS 0.006 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.19 (33893) covalent geometry : angle 0.64859 / 0.38 (48801) hydrogen bonds : bond 0.06537 / 4.38 ( 2057) hydrogen bonds : angle 3.13541 / 2.28 ( 5220) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 269 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.6803 (mm-30) cc_final: 0.6496 (mm-30) REVERT: C 32 ARG cc_start: 0.6125 (OUTLIER) cc_final: 0.5662 (ptt180) REVERT: D 61 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.7993 (mp) REVERT: D 93 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6488 (mp0) REVERT: G 56 GLU cc_start: 0.6528 (mt-10) cc_final: 0.6206 (mm-30) REVERT: G 118 LYS cc_start: 0.3941 (OUTLIER) cc_final: 0.2768 (tmmm) REVERT: H 51 ASP cc_start: 0.6554 (p0) cc_final: 0.6195 (t70) REVERT: K 133 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6175 (mp0) REVERT: N 46 LYS cc_start: 0.6069 (tttt) cc_final: 0.5402 (mtpt) REVERT: R 39 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7786 (tp) REVERT: R 76 GLU cc_start: 0.7382 (tp30) cc_final: 0.7098 (tp30) REVERT: R 88 THR cc_start: 0.7106 (m) cc_final: 0.6801 (p) REVERT: U 64 LYS cc_start: 0.7743 (mttm) cc_final: 0.7365 (mtpp) REVERT: U 129 ARG cc_start: 0.7676 (ttm-80) cc_final: 0.7362 (ttt90) REVERT: V 85 ASP cc_start: 0.7973 (m-30) cc_final: 0.7685 (m-30) REVERT: V 93 GLN cc_start: 0.7167 (mp10) cc_final: 0.6955 (mp10) REVERT: W 95 LYS cc_start: 0.8024 (tttp) cc_final: 0.7696 (tttp) REVERT: X 42 TYR cc_start: 0.7182 (t80) cc_final: 0.6819 (t80) REVERT: Y 79 LYS cc_start: 0.6523 (tttt) cc_final: 0.6020 (tptt) REVERT: Z 88 TYR cc_start: 0.7300 (m-10) cc_final: 0.6994 (m-10) REVERT: b 43 LYS cc_start: 0.7011 (mttt) cc_final: 0.6499 (mtpp) outliers start: 79 outliers final: 60 residues processed: 329 average time/residue: 0.2228 time to fit residues: 114.0030 Evaluate side-chains 325 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 259 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 32 ARG Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 133 GLU Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 92 ARG Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain O residue 62 ILE Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain W residue 79 ILE Chi-restraints excluded: chain W residue 101 THR Chi-restraints excluded: chain X residue 51 ASP Chi-restraints excluded: chain X residue 52 THR Chi-restraints excluded: chain X residue 57 LYS Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 101 LEU Chi-restraints excluded: chain X residue 112 SER Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 70 VAL Chi-restraints excluded: chain Z residue 73 THR Chi-restraints excluded: chain Z residue 82 THR Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 75 LYS Chi-restraints excluded: chain a residue 76 THR Chi-restraints excluded: chain b residue 51 ASP Chi-restraints excluded: chain b residue 54 ILE Chi-restraints excluded: chain b residue 90 THR Chi-restraints excluded: chain b residue 94 ILE Chi-restraints excluded: chain b residue 119 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 96 optimal weight: 3.9990 chunk 209 optimal weight: 6.9990 chunk 252 optimal weight: 50.0000 chunk 62 optimal weight: 0.9990 chunk 75 optimal weight: 50.0000 chunk 65 optimal weight: 4.9990 chunk 212 optimal weight: 7.9990 chunk 69 optimal weight: 50.0000 chunk 63 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 247 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN M 68 ASN ** Q 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 110 ASN b 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.141353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.105705 restraints weight = 61765.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.105912 restraints weight = 68865.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.106192 restraints weight = 68783.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.106409 restraints weight = 59890.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.106613 restraints weight = 56242.696| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33893 Z= 0.168 Angle : 0.604 8.630 48801 Z= 0.359 Chirality : 0.043 0.322 5566 Planarity : 0.004 0.048 3717 Dihedral : 29.483 89.964 10137 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.55 % Allowed : 15.14 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.18), residues: 2139 helix: 2.42 (0.13), residues: 1518 sheet: None (None), residues: 0 loop : -1.51 (0.23), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG Z 78 TYR 0.052 0.002 TYR F 88 PHE 0.011 0.002 PHE A 67 HIS 0.004 0.001 HIS N 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.17 (33893) covalent geometry : angle 0.60445 / 0.36 (48801) hydrogen bonds : bond 0.05908 / 3.96 ( 2057) hydrogen bonds : angle 3.01500 / 2.20 ( 5220) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 273 time to evaluate : 0.901 Fit side-chains REVERT: B 17 ARG cc_start: 0.1625 (OUTLIER) cc_final: -0.0380 (mmp-170) REVERT: C 32 ARG cc_start: 0.6125 (OUTLIER) cc_final: 0.5686 (ptt180) REVERT: D 61 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7954 (mp) REVERT: D 92 ARG cc_start: 0.5800 (mtp85) cc_final: 0.5588 (mtp180) REVERT: G 118 LYS cc_start: 0.3807 (OUTLIER) cc_final: 0.2645 (tmmm) REVERT: H 51 ASP cc_start: 0.6432 (p0) cc_final: 0.6114 (t70) REVERT: K 133 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6170 (mp0) REVERT: N 46 LYS cc_start: 0.5906 (tttt) cc_final: 0.5336 (mtpt) REVERT: N 84 ASN cc_start: 0.7875 (OUTLIER) cc_final: 0.7553 (m110) REVERT: R 39 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7816 (tp) REVERT: R 76 GLU cc_start: 0.7399 (tp30) cc_final: 0.7128 (tp30) REVERT: U 64 LYS cc_start: 0.7709 (mttm) cc_final: 0.7350 (mtpp) REVERT: U 129 ARG cc_start: 0.7671 (ttm-80) cc_final: 0.7342 (ttt90) REVERT: V 85 ASP cc_start: 0.7941 (m-30) cc_final: 0.7676 (m-30) REVERT: W 95 LYS cc_start: 0.8035 (tttp) cc_final: 0.7704 (tttp) REVERT: X 42 TYR cc_start: 0.7115 (t80) cc_final: 0.6787 (t80) REVERT: b 43 LYS cc_start: 0.7017 (mttt) cc_final: 0.6481 (mtpp) outliers start: 65 outliers final: 54 residues processed: 321 average time/residue: 0.2285 time to fit residues: 113.9916 Evaluate side-chains 325 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 264 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 17 ARG Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain C residue 32 ARG Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 133 GLU Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain O residue 62 ILE Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain V residue 80 THR Chi-restraints excluded: chain W residue 79 ILE Chi-restraints excluded: chain W residue 101 THR Chi-restraints excluded: chain X residue 52 THR Chi-restraints excluded: chain X residue 57 LYS Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 101 LEU Chi-restraints excluded: chain X residue 112 SER Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain Z residue 21 VAL Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 73 THR Chi-restraints excluded: chain Z residue 82 THR Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 75 LYS Chi-restraints excluded: chain b residue 54 ILE Chi-restraints excluded: chain b residue 94 ILE Chi-restraints excluded: chain b residue 119 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 11 optimal weight: 10.0000 chunk 248 optimal weight: 8.9990 chunk 63 optimal weight: 0.6980 chunk 201 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 86 optimal weight: 50.0000 chunk 162 optimal weight: 30.0000 chunk 145 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 202 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN G 112 GLN K 68 GLN L 25 ASN L 27 GLN ** Q 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 75 HIS X 84 ASN Y 93 GLN a 110 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.141869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.106465 restraints weight = 61634.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.106553 restraints weight = 71991.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.106928 restraints weight = 69414.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.107144 restraints weight = 59500.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.107339 restraints weight = 57465.107| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33893 Z= 0.150 Angle : 0.577 8.054 48801 Z= 0.347 Chirality : 0.041 0.303 5566 Planarity : 0.004 0.055 3717 Dihedral : 29.444 89.653 10137 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.28 % Allowed : 15.53 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.18), residues: 2139 helix: 2.55 (0.13), residues: 1517 sheet: None (None), residues: 0 loop : -1.43 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG Z 78 TYR 0.061 0.002 TYR F 88 PHE 0.010 0.001 PHE D 65 HIS 0.003 0.001 HIS N 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.15 (33893) covalent geometry : angle 0.57737 / 0.35 (48801) hydrogen bonds : bond 0.05444 / 3.65 ( 2057) hydrogen bonds : angle 2.92245 / 2.13 ( 5220) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 274 time to evaluate : 0.928 Fit side-chains REVERT: B 17 ARG cc_start: 0.1608 (OUTLIER) cc_final: 0.1349 (mmp-170) REVERT: C 32 ARG cc_start: 0.6036 (OUTLIER) cc_final: 0.5610 (ptt180) REVERT: C 35 ARG cc_start: 0.7491 (mmt180) cc_final: 0.7145 (mmm-85) REVERT: D 61 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7876 (mp) REVERT: D 93 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6487 (mp0) REVERT: G 56 GLU cc_start: 0.6468 (mt-10) cc_final: 0.6087 (mm-30) REVERT: G 118 LYS cc_start: 0.3769 (OUTLIER) cc_final: 0.2612 (tmmm) REVERT: H 51 ASP cc_start: 0.6536 (p0) cc_final: 0.6154 (t70) REVERT: K 133 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6147 (mp0) REVERT: N 46 LYS cc_start: 0.5915 (tttt) cc_final: 0.5330 (mtpt) REVERT: R 39 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7798 (tp) REVERT: R 76 GLU cc_start: 0.7425 (tp30) cc_final: 0.7144 (tp30) REVERT: U 64 LYS cc_start: 0.7628 (mttm) cc_final: 0.7258 (mtpp) REVERT: U 129 ARG cc_start: 0.7667 (ttm-80) cc_final: 0.7330 (ttt90) REVERT: V 85 ASP cc_start: 0.7918 (m-30) cc_final: 0.7641 (m-30) REVERT: W 95 LYS cc_start: 0.8034 (tttp) cc_final: 0.7715 (tttp) REVERT: X 42 TYR cc_start: 0.7099 (t80) cc_final: 0.6775 (t80) REVERT: Z 84 MET cc_start: 0.7109 (tmm) cc_final: 0.6890 (tmm) REVERT: a 71 ARG cc_start: 0.6198 (tpt170) cc_final: 0.4765 (mtt180) REVERT: b 43 LYS cc_start: 0.7084 (mttt) cc_final: 0.6519 (mtpp) outliers start: 60 outliers final: 46 residues processed: 320 average time/residue: 0.2315 time to fit residues: 114.4706 Evaluate side-chains 320 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 267 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 17 ARG Chi-restraints excluded: chain C residue 32 ARG Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 133 GLU Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain O residue 62 ILE Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain V residue 80 THR Chi-restraints excluded: chain W residue 79 ILE Chi-restraints excluded: chain W residue 101 THR Chi-restraints excluded: chain X residue 52 THR Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 101 LEU Chi-restraints excluded: chain X residue 112 SER Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 73 THR Chi-restraints excluded: chain Z residue 82 THR Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 75 LYS Chi-restraints excluded: chain b residue 54 ILE Chi-restraints excluded: chain b residue 94 ILE Chi-restraints excluded: chain b residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 217 optimal weight: 0.0980 chunk 43 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 253 optimal weight: 40.0000 chunk 146 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 241 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 78 optimal weight: 50.0000 chunk 71 optimal weight: 30.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN L 25 ASN L 27 GLN ** Q 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 93 GLN a 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.141699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.106367 restraints weight = 61929.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.106371 restraints weight = 75658.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.106759 restraints weight = 71989.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.106987 restraints weight = 62504.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.107210 restraints weight = 58924.002| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33893 Z= 0.154 Angle : 0.585 8.328 48801 Z= 0.349 Chirality : 0.041 0.299 5566 Planarity : 0.004 0.051 3717 Dihedral : 29.467 89.832 10137 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.39 % Allowed : 15.25 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.18), residues: 2139 helix: 2.53 (0.13), residues: 1515 sheet: None (None), residues: 0 loop : -1.45 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG Z 78 TYR 0.072 0.002 TYR F 88 PHE 0.012 0.001 PHE A 67 HIS 0.004 0.001 HIS N 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 (33893) covalent geometry : angle 0.58521 / 0.35 (48801) hydrogen bonds : bond 0.05543 / 3.72 ( 2057) hydrogen bonds : angle 2.93563 / 2.14 ( 5220) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 271 time to evaluate : 0.852 Fit side-chains REVERT: B 17 ARG cc_start: 0.1446 (OUTLIER) cc_final: 0.1136 (mmp-170) REVERT: C 32 ARG cc_start: 0.6019 (OUTLIER) cc_final: 0.5633 (ptt180) REVERT: D 61 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7903 (mp) REVERT: D 93 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6439 (mp0) REVERT: G 56 GLU cc_start: 0.6477 (mm-30) cc_final: 0.6094 (mm-30) REVERT: G 118 LYS cc_start: 0.3883 (OUTLIER) cc_final: 0.2719 (tmmm) REVERT: H 51 ASP cc_start: 0.6532 (p0) cc_final: 0.6120 (t70) REVERT: K 133 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6137 (mp0) REVERT: N 46 LYS cc_start: 0.5937 (tttt) cc_final: 0.5344 (mtpt) REVERT: R 39 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7831 (tp) REVERT: R 76 GLU cc_start: 0.7384 (tp30) cc_final: 0.7111 (tp30) REVERT: U 64 LYS cc_start: 0.7647 (mttm) cc_final: 0.7281 (mtpp) REVERT: U 129 ARG cc_start: 0.7606 (ttm-80) cc_final: 0.7276 (ttt90) REVERT: V 85 ASP cc_start: 0.7883 (m-30) cc_final: 0.7630 (m-30) REVERT: W 95 LYS cc_start: 0.8016 (tttp) cc_final: 0.7701 (tttp) REVERT: X 42 TYR cc_start: 0.7092 (t80) cc_final: 0.6765 (t80) REVERT: a 71 ARG cc_start: 0.6262 (tpt170) cc_final: 0.4825 (mtt180) REVERT: b 43 LYS cc_start: 0.7077 (mttt) cc_final: 0.6523 (mtpp) outliers start: 62 outliers final: 54 residues processed: 318 average time/residue: 0.2201 time to fit residues: 109.0645 Evaluate side-chains 329 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 268 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 17 ARG Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain C residue 32 ARG Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 133 GLU Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain O residue 62 ILE Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain V residue 80 THR Chi-restraints excluded: chain W residue 79 ILE Chi-restraints excluded: chain W residue 101 THR Chi-restraints excluded: chain X residue 51 ASP Chi-restraints excluded: chain X residue 52 THR Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 101 LEU Chi-restraints excluded: chain X residue 112 SER Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain Z residue 21 VAL Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 73 THR Chi-restraints excluded: chain Z residue 82 THR Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 75 LYS Chi-restraints excluded: chain a residue 76 THR Chi-restraints excluded: chain b residue 54 ILE Chi-restraints excluded: chain b residue 94 ILE Chi-restraints excluded: chain b residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 135 optimal weight: 10.0000 chunk 255 optimal weight: 30.0000 chunk 128 optimal weight: 10.0000 chunk 172 optimal weight: 50.0000 chunk 246 optimal weight: 0.8980 chunk 116 optimal weight: 0.3980 chunk 242 optimal weight: 0.9990 chunk 189 optimal weight: 1.9990 chunk 74 optimal weight: 40.0000 chunk 262 optimal weight: 50.0000 chunk 44 optimal weight: 6.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN L 27 GLN ** Q 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 93 GLN a 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.141685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.106366 restraints weight = 61874.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.106430 restraints weight = 72594.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.106795 restraints weight = 70501.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.107016 restraints weight = 61339.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.107222 restraints weight = 57954.928| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.238 33893 Z= 0.182 Angle : 0.687 59.198 48801 Z= 0.419 Chirality : 0.041 0.299 5566 Planarity : 0.004 0.049 3717 Dihedral : 29.467 89.841 10137 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.61 % Allowed : 15.04 % Favored : 81.36 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.18), residues: 2139 helix: 2.54 (0.13), residues: 1515 sheet: None (None), residues: 0 loop : -1.46 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG Z 78 TYR 0.063 0.002 TYR F 88 PHE 0.011 0.001 PHE A 67 HIS 0.004 0.001 HIS N 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.18 (33893) covalent geometry : angle 0.68691 / 0.42 (48801) hydrogen bonds : bond 0.05523 / 3.70 ( 2057) hydrogen bonds : angle 2.93394 / 2.13 ( 5220) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4551.64 seconds wall clock time: 79 minutes 31.51 seconds (4771.51 seconds total)