Starting phenix.real_space_refine on Sun Feb 8 03:28:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m8o_63716/02_2026/9m8o_63716.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m8o_63716/02_2026/9m8o_63716.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m8o_63716/02_2026/9m8o_63716.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m8o_63716/02_2026/9m8o_63716.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m8o_63716/02_2026/9m8o_63716.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m8o_63716/02_2026/9m8o_63716.map" } resolution = 3.44 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 113 5.16 5 C 25524 2.51 5 N 6600 2.21 5 O 7968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40205 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 1297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1297 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain: "B" Number of atoms: 1297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1297 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain: "C" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1285 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 Chain: "D" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1281 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain: "E" Number of atoms: 1297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1297 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain: "F" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1292 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain: "G" Number of atoms: 2023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2023 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 7, 'TRANS': 247} Chain: "H" Number of atoms: 2023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2023 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 7, 'TRANS': 247} Chain: "I" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2015 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "J" Number of atoms: 1986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1986 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 7, 'TRANS': 242} Chain: "K" Number of atoms: 1986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1986 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 7, 'TRANS': 242} Chain: "L" Number of atoms: 1986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1986 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 7, 'TRANS': 242} Chain: "M" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 220 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "N" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 220 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "O" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 209 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "P" Number of atoms: 1246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1246 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 3, 'TRANS': 152} Chain: "Q" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1259 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 3, 'TRANS': 154} Chain: "R" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 793 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain breaks: 2 Chain: "S" Number of atoms: 1246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1246 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 3, 'TRANS': 152} Chain: "T" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1259 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 3, 'TRANS': 154} Chain: "U" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 793 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain breaks: 2 Chain: "V" Number of atoms: 1246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1246 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 3, 'TRANS': 152} Chain: "W" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1259 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 3, 'TRANS': 154} Chain: "X" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 793 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain breaks: 2 Chain: "Y" Number of atoms: 1246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1246 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 3, 'TRANS': 152} Chain: "Z" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1259 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 3, 'TRANS': 154} Chain: "a" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 793 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain breaks: 2 Chain: "b" Number of atoms: 1246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1246 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 3, 'TRANS': 152} Chain: "c" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1259 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 3, 'TRANS': 154} Chain: "d" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 793 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain breaks: 2 Chain: "e" Number of atoms: 1246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1246 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 3, 'TRANS': 152} Chain: "f" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1259 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 3, 'TRANS': 154} Chain: "g" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 793 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain breaks: 2 Time building chain proxies: 8.57, per 1000 atoms: 0.21 Number of scatterers: 40205 At special positions: 0 Unit cell: (231.6, 218.4, 214.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 113 16.00 O 7968 8.00 N 6600 7.00 C 25524 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: 3.19 Conformation dependent library (CDL) restraints added in 1.6 seconds 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9642 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 61 sheets defined 17.3% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 6 through 8 No H-bonds generated for 'chain 'A' and resid 6 through 8' Processing helix chain 'A' and resid 18 through 20 No H-bonds generated for 'chain 'A' and resid 18 through 20' Processing helix chain 'A' and resid 73 through 85 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'B' and resid 6 through 8 No H-bonds generated for 'chain 'B' and resid 6 through 8' Processing helix chain 'B' and resid 18 through 20 No H-bonds generated for 'chain 'B' and resid 18 through 20' Processing helix chain 'B' and resid 73 through 85 Processing helix chain 'C' and resid 6 through 8 No H-bonds generated for 'chain 'C' and resid 6 through 8' Processing helix chain 'C' and resid 18 through 20 No H-bonds generated for 'chain 'C' and resid 18 through 20' Processing helix chain 'C' and resid 73 through 85 Processing helix chain 'D' and resid 6 through 8 No H-bonds generated for 'chain 'D' and resid 6 through 8' Processing helix chain 'D' and resid 18 through 20 No H-bonds generated for 'chain 'D' and resid 18 through 20' Processing helix chain 'D' and resid 73 through 85 Processing helix chain 'E' and resid 6 through 8 No H-bonds generated for 'chain 'E' and resid 6 through 8' Processing helix chain 'E' and resid 18 through 20 No H-bonds generated for 'chain 'E' and resid 18 through 20' Processing helix chain 'E' and resid 73 through 85 Processing helix chain 'F' and resid 6 through 8 No H-bonds generated for 'chain 'F' and resid 6 through 8' Processing helix chain 'F' and resid 18 through 20 No H-bonds generated for 'chain 'F' and resid 18 through 20' Processing helix chain 'F' and resid 73 through 85 Processing helix chain 'G' and resid 30 through 34 Processing helix chain 'G' and resid 83 through 99 Processing helix chain 'H' and resid 30 through 34 Processing helix chain 'H' and resid 83 through 99 removed outlier: 3.686A pdb=" N ILE H 87 " --> pdb=" O SER H 83 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLN H 88 " --> pdb=" O SER H 84 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP H 89 " --> pdb=" O GLN H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 219 through 222 Processing helix chain 'I' and resid 30 through 34 Processing helix chain 'I' and resid 83 through 99 removed outlier: 3.675A pdb=" N ILE I 87 " --> pdb=" O SER I 83 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLN I 88 " --> pdb=" O SER I 84 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP I 89 " --> pdb=" O GLN I 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 33 No H-bonds generated for 'chain 'J' and resid 31 through 33' Processing helix chain 'J' and resid 85 through 99 removed outlier: 3.834A pdb=" N ASP J 89 " --> pdb=" O GLN J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 219 through 222 Processing helix chain 'K' and resid 83 through 99 removed outlier: 3.630A pdb=" N ILE K 87 " --> pdb=" O SER K 83 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN K 88 " --> pdb=" O SER K 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 34 removed outlier: 3.529A pdb=" N ILE L 34 " --> pdb=" O LEU L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 99 removed outlier: 3.816A pdb=" N ILE L 87 " --> pdb=" O SER L 83 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN L 88 " --> pdb=" O SER L 84 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP L 89 " --> pdb=" O GLN L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 219 through 222 Processing helix chain 'M' and resid 651 through 673 removed outlier: 3.923A pdb=" N TYR M 655 " --> pdb=" O GLN M 651 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE M 656 " --> pdb=" O ASP M 652 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU M 672 " --> pdb=" O ALA M 668 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN M 673 " --> pdb=" O GLN M 669 " (cutoff:3.500A) Processing helix chain 'N' and resid 650 through 674 removed outlier: 3.624A pdb=" N LYS N 654 " --> pdb=" O LYS N 650 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR N 655 " --> pdb=" O GLN N 651 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE N 656 " --> pdb=" O ASP N 652 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN N 673 " --> pdb=" O GLN N 669 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE N 674 " --> pdb=" O ILE N 670 " (cutoff:3.500A) Processing helix chain 'O' and resid 650 through 673 removed outlier: 3.741A pdb=" N LYS O 654 " --> pdb=" O LYS O 650 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR O 655 " --> pdb=" O GLN O 651 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE O 656 " --> pdb=" O ASP O 652 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN O 673 " --> pdb=" O GLN O 669 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 53 Processing helix chain 'P' and resid 88 through 93 removed outlier: 3.790A pdb=" N LEU P 92 " --> pdb=" O PRO P 88 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS P 93 " --> pdb=" O ARG P 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 88 through 93' Processing helix chain 'P' and resid 126 through 130 removed outlier: 3.834A pdb=" N PHE P 130 " --> pdb=" O MET P 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 131 through 158 removed outlier: 3.760A pdb=" N LYS P 135 " --> pdb=" O SER P 131 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN P 151 " --> pdb=" O THR P 147 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG P 152 " --> pdb=" O LYS P 148 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL P 153 " --> pdb=" O ILE P 149 " (cutoff:3.500A) Processing helix chain 'Q' and resid 89 through 94 Processing helix chain 'Q' and resid 140 through 160 removed outlier: 3.684A pdb=" N ILE Q 160 " --> pdb=" O ILE Q 156 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 162 removed outlier: 3.642A pdb=" N LEU R 145 " --> pdb=" O THR R 141 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG R 152 " --> pdb=" O LYS R 148 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN R 162 " --> pdb=" O GLU R 158 " (cutoff:3.500A) Processing helix chain 'S' and resid 50 through 53 Processing helix chain 'S' and resid 89 through 94 removed outlier: 3.552A pdb=" N HIS S 94 " --> pdb=" O PHE S 91 " (cutoff:3.500A) Processing helix chain 'S' and resid 126 through 130 removed outlier: 3.907A pdb=" N PHE S 130 " --> pdb=" O MET S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 131 through 158 removed outlier: 3.762A pdb=" N LYS S 135 " --> pdb=" O SER S 131 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN S 151 " --> pdb=" O THR S 147 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG S 152 " --> pdb=" O LYS S 148 " (cutoff:3.500A) Processing helix chain 'T' and resid 90 through 94 Processing helix chain 'T' and resid 140 through 160 Processing helix chain 'U' and resid 141 through 162 removed outlier: 3.516A pdb=" N LEU U 145 " --> pdb=" O THR U 141 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG U 152 " --> pdb=" O LYS U 148 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASN U 162 " --> pdb=" O GLU U 158 " (cutoff:3.500A) Processing helix chain 'V' and resid 50 through 54 Processing helix chain 'V' and resid 88 through 93 removed outlier: 3.786A pdb=" N LEU V 92 " --> pdb=" O PRO V 88 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS V 93 " --> pdb=" O ARG V 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 88 through 93' Processing helix chain 'V' and resid 126 through 130 removed outlier: 3.758A pdb=" N PHE V 130 " --> pdb=" O MET V 127 " (cutoff:3.500A) Processing helix chain 'V' and resid 131 through 153 removed outlier: 3.747A pdb=" N LYS V 135 " --> pdb=" O SER V 131 " (cutoff:3.500A) Processing helix chain 'V' and resid 153 through 158 Processing helix chain 'W' and resid 90 through 94 Processing helix chain 'W' and resid 140 through 160 removed outlier: 3.731A pdb=" N ILE W 160 " --> pdb=" O ILE W 156 " (cutoff:3.500A) Processing helix chain 'X' and resid 141 through 162 removed outlier: 3.635A pdb=" N LEU X 145 " --> pdb=" O THR X 141 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG X 152 " --> pdb=" O LYS X 148 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN X 162 " --> pdb=" O GLU X 158 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 53 Processing helix chain 'Y' and resid 89 through 94 removed outlier: 3.589A pdb=" N HIS Y 94 " --> pdb=" O PHE Y 91 " (cutoff:3.500A) Processing helix chain 'Y' and resid 126 through 130 removed outlier: 3.981A pdb=" N PHE Y 130 " --> pdb=" O MET Y 127 " (cutoff:3.500A) Processing helix chain 'Y' and resid 131 through 158 removed outlier: 3.722A pdb=" N LYS Y 135 " --> pdb=" O SER Y 131 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLU Y 154 " --> pdb=" O LYS Y 150 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ALA Y 155 " --> pdb=" O GLN Y 151 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE Y 156 " --> pdb=" O ARG Y 152 " (cutoff:3.500A) Processing helix chain 'Z' and resid 90 through 94 Processing helix chain 'Z' and resid 140 through 160 removed outlier: 3.529A pdb=" N ILE Z 160 " --> pdb=" O ILE Z 156 " (cutoff:3.500A) Processing helix chain 'a' and resid 141 through 162 removed outlier: 3.572A pdb=" N LEU a 145 " --> pdb=" O THR a 141 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN a 162 " --> pdb=" O GLU a 158 " (cutoff:3.500A) Processing helix chain 'b' and resid 50 through 53 Processing helix chain 'b' and resid 88 through 93 removed outlier: 3.797A pdb=" N LEU b 92 " --> pdb=" O PRO b 88 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS b 93 " --> pdb=" O ARG b 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 88 through 93' Processing helix chain 'b' and resid 126 through 130 removed outlier: 3.773A pdb=" N PHE b 130 " --> pdb=" O MET b 127 " (cutoff:3.500A) Processing helix chain 'b' and resid 131 through 158 removed outlier: 3.751A pdb=" N LYS b 135 " --> pdb=" O SER b 131 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU b 154 " --> pdb=" O LYS b 150 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ALA b 155 " --> pdb=" O GLN b 151 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ILE b 156 " --> pdb=" O ARG b 152 " (cutoff:3.500A) Processing helix chain 'c' and resid 90 through 94 Processing helix chain 'c' and resid 140 through 160 removed outlier: 3.750A pdb=" N ILE c 160 " --> pdb=" O ILE c 156 " (cutoff:3.500A) Processing helix chain 'd' and resid 141 through 162 removed outlier: 3.712A pdb=" N ARG d 152 " --> pdb=" O LYS d 148 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN d 162 " --> pdb=" O GLU d 158 " (cutoff:3.500A) Processing helix chain 'e' and resid 50 through 53 Processing helix chain 'e' and resid 88 through 94 removed outlier: 3.579A pdb=" N LYS e 93 " --> pdb=" O GLU e 90 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS e 94 " --> pdb=" O PHE e 91 " (cutoff:3.500A) Processing helix chain 'e' and resid 126 through 130 removed outlier: 3.945A pdb=" N PHE e 130 " --> pdb=" O MET e 127 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 158 removed outlier: 3.789A pdb=" N LYS e 135 " --> pdb=" O SER e 131 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLU e 154 " --> pdb=" O LYS e 150 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ALA e 155 " --> pdb=" O GLN e 151 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE e 156 " --> pdb=" O ARG e 152 " (cutoff:3.500A) Processing helix chain 'f' and resid 90 through 94 Processing helix chain 'f' and resid 140 through 160 removed outlier: 3.544A pdb=" N ILE f 160 " --> pdb=" O ILE f 156 " (cutoff:3.500A) Processing helix chain 'g' and resid 141 through 162 removed outlier: 3.577A pdb=" N LEU g 145 " --> pdb=" O THR g 141 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG g 152 " --> pdb=" O LYS g 148 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN g 162 " --> pdb=" O GLU g 158 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 16 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 26 through 27 current: chain 'A' and resid 51 through 67 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 51 through 67 current: chain 'A' and resid 107 through 121 removed outlier: 6.057A pdb=" N GLU A 134 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE A 119 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLU A 132 " --> pdb=" O PHE A 119 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS A 121 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU A 130 " --> pdb=" O LYS A 121 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 130 through 137 current: chain 'B' and resid 26 through 27 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 26 through 27 current: chain 'B' and resid 51 through 67 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 51 through 67 current: chain 'B' and resid 107 through 121 removed outlier: 6.065A pdb=" N GLU B 134 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N PHE B 119 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLU B 132 " --> pdb=" O PHE B 119 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LYS B 121 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLU B 130 " --> pdb=" O LYS B 121 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 130 through 137 current: chain 'C' and resid 26 through 27 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 26 through 27 current: chain 'C' and resid 50 through 67 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 50 through 67 current: chain 'C' and resid 107 through 108 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 107 through 108 current: chain 'C' and resid 130 through 137 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 130 through 137 current: chain 'D' and resid 26 through 27 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 26 through 27 current: chain 'D' and resid 50 through 67 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 50 through 67 current: chain 'D' and resid 107 through 121 removed outlier: 3.573A pdb=" N ALA D 136 " --> pdb=" O TYR D 115 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLU D 134 " --> pdb=" O SER D 117 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE D 119 " --> pdb=" O GLU D 132 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLU D 132 " --> pdb=" O PHE D 119 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LYS D 121 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N GLU D 130 " --> pdb=" O LYS D 121 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 130 through 137 current: chain 'E' and resid 26 through 27 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 26 through 27 current: chain 'E' and resid 51 through 67 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 51 through 67 current: chain 'E' and resid 106 through 121 removed outlier: 5.991A pdb=" N GLU E 134 " --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE E 119 " --> pdb=" O GLU E 132 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLU E 132 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LYS E 121 " --> pdb=" O GLU E 130 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N GLU E 130 " --> pdb=" O LYS E 121 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 130 through 137 current: chain 'F' and resid 26 through 27 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 26 through 27 current: chain 'F' and resid 51 through 67 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 51 through 67 current: chain 'F' and resid 107 through 121 removed outlier: 6.095A pdb=" N GLU F 134 " --> pdb=" O SER F 117 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE F 119 " --> pdb=" O GLU F 132 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLU F 132 " --> pdb=" O PHE F 119 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LYS F 121 " --> pdb=" O GLU F 130 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLU F 130 " --> pdb=" O LYS F 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 28 through 29 removed outlier: 5.845A pdb=" N TYR G 120 " --> pdb=" O PHE G 140 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N PHE G 140 " --> pdb=" O TYR G 120 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER G 122 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER G 135 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N THR G 74 " --> pdb=" O VAL G 42 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N VAL G 42 " --> pdb=" O THR G 74 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N THR G 76 " --> pdb=" O LEU G 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 50 through 56 removed outlier: 3.565A pdb=" N ASP G 53 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY G 65 " --> pdb=" O ASP G 53 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N THR G 55 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N VAL G 63 " --> pdb=" O THR G 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 151 through 153 removed outlier: 3.862A pdb=" N LYS G 169 " --> pdb=" O TYR G 249 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL G 202 " --> pdb=" O THR G 172 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 187 through 196 removed outlier: 7.417A pdb=" N ARG G 193 " --> pdb=" O GLY G 178 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N GLY G 178 " --> pdb=" O ARG G 193 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 28 through 29 removed outlier: 5.816A pdb=" N TYR H 120 " --> pdb=" O PHE H 140 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N PHE H 140 " --> pdb=" O TYR H 120 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER H 122 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER H 135 " --> pdb=" O TYR H 77 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N THR H 74 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL H 42 " --> pdb=" O THR H 74 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N THR H 76 " --> pdb=" O LEU H 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 50 through 57 removed outlier: 6.814A pdb=" N THR H 51 " --> pdb=" O GLN H 66 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLN H 66 " --> pdb=" O THR H 51 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASP H 53 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY H 60 " --> pdb=" O VAL H 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 150 through 153 removed outlier: 3.820A pdb=" N LYS H 169 " --> pdb=" O TYR H 249 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL H 202 " --> pdb=" O THR H 172 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 188 through 196 removed outlier: 7.749A pdb=" N ARG H 193 " --> pdb=" O GLY H 178 " (cutoff:3.500A) removed outlier: 9.344A pdb=" N GLY H 178 " --> pdb=" O ARG H 193 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 28 through 29 removed outlier: 3.596A pdb=" N GLY I 118 " --> pdb=" O VAL I 104 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N PHE I 108 " --> pdb=" O THR I 114 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N THR I 114 " --> pdb=" O PHE I 108 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N TYR I 120 " --> pdb=" O PHE I 140 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N PHE I 140 " --> pdb=" O TYR I 120 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER I 122 " --> pdb=" O THR I 138 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER I 135 " --> pdb=" O TYR I 77 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N THR I 74 " --> pdb=" O VAL I 42 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL I 42 " --> pdb=" O THR I 74 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR I 76 " --> pdb=" O LEU I 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 50 through 56 removed outlier: 6.753A pdb=" N THR I 51 " --> pdb=" O GLN I 66 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLN I 66 " --> pdb=" O THR I 51 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASP I 53 " --> pdb=" O ASN I 64 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 151 through 153 removed outlier: 3.862A pdb=" N LYS I 169 " --> pdb=" O TYR I 249 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS I 210 " --> pdb=" O ASP I 205 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 187 through 196 removed outlier: 7.556A pdb=" N ARG I 193 " --> pdb=" O GLY I 178 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N GLY I 178 " --> pdb=" O ARG I 193 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 28 through 29 removed outlier: 3.615A pdb=" N GLY J 118 " --> pdb=" O VAL J 104 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N PHE J 108 " --> pdb=" O THR J 114 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR J 114 " --> pdb=" O PHE J 108 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N TYR J 120 " --> pdb=" O PHE J 140 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N PHE J 140 " --> pdb=" O TYR J 120 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER J 122 " --> pdb=" O THR J 138 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER J 135 " --> pdb=" O TYR J 77 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR J 74 " --> pdb=" O VAL J 42 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL J 42 " --> pdb=" O THR J 74 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR J 76 " --> pdb=" O LEU J 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 50 through 57 removed outlier: 6.772A pdb=" N THR J 51 " --> pdb=" O GLN J 66 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLN J 66 " --> pdb=" O THR J 51 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ASP J 53 " --> pdb=" O ASN J 64 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY J 60 " --> pdb=" O VAL J 57 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 151 through 153 removed outlier: 3.567A pdb=" N TYR J 250 " --> pdb=" O ILE J 151 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS J 169 " --> pdb=" O TYR J 249 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL J 202 " --> pdb=" O THR J 172 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS J 210 " --> pdb=" O ASP J 205 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 187 through 196 removed outlier: 3.505A pdb=" N MET J 180 " --> pdb=" O MET J 191 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ARG J 193 " --> pdb=" O GLY J 178 " (cutoff:3.500A) removed outlier: 9.944A pdb=" N GLY J 178 " --> pdb=" O ARG J 193 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 28 through 29 removed outlier: 3.593A pdb=" N GLY K 118 " --> pdb=" O VAL K 104 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N TYR K 120 " --> pdb=" O PHE K 140 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N PHE K 140 " --> pdb=" O TYR K 120 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER K 122 " --> pdb=" O THR K 138 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER K 135 " --> pdb=" O TYR K 77 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR K 74 " --> pdb=" O VAL K 42 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL K 42 " --> pdb=" O THR K 74 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR K 76 " --> pdb=" O LEU K 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 50 through 57 removed outlier: 6.620A pdb=" N THR K 51 " --> pdb=" O GLN K 66 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLN K 66 " --> pdb=" O THR K 51 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ASP K 53 " --> pdb=" O ASN K 64 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN K 64 " --> pdb=" O ASP K 53 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY K 60 " --> pdb=" O VAL K 57 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 151 through 153 removed outlier: 3.608A pdb=" N TYR K 250 " --> pdb=" O ILE K 151 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS K 169 " --> pdb=" O TYR K 249 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS K 210 " --> pdb=" O ASP K 205 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 188 through 196 removed outlier: 3.573A pdb=" N MET K 180 " --> pdb=" O MET K 191 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ARG K 193 " --> pdb=" O GLY K 178 " (cutoff:3.500A) removed outlier: 9.952A pdb=" N GLY K 178 " --> pdb=" O ARG K 193 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 23 through 25 removed outlier: 3.528A pdb=" N VAL L 104 " --> pdb=" O GLY L 118 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY L 118 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N PHE L 108 " --> pdb=" O THR L 114 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N THR L 114 " --> pdb=" O PHE L 108 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR L 120 " --> pdb=" O PHE L 140 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N PHE L 140 " --> pdb=" O TYR L 120 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER L 122 " --> pdb=" O THR L 138 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER L 135 " --> pdb=" O TYR L 77 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR L 74 " --> pdb=" O VAL L 42 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL L 42 " --> pdb=" O THR L 74 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR L 76 " --> pdb=" O LEU L 40 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 50 through 57 removed outlier: 6.516A pdb=" N THR L 51 " --> pdb=" O GLN L 66 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLN L 66 " --> pdb=" O THR L 51 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ASP L 53 " --> pdb=" O ASN L 64 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN L 64 " --> pdb=" O ASP L 53 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY L 60 " --> pdb=" O VAL L 57 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 151 through 153 removed outlier: 3.537A pdb=" N TYR L 250 " --> pdb=" O ILE L 151 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS L 169 " --> pdb=" O TYR L 249 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS L 210 " --> pdb=" O ASP L 205 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 178 through 183 removed outlier: 9.922A pdb=" N GLY L 178 " --> pdb=" O ARG L 193 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ARG L 193 " --> pdb=" O GLY L 178 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'P' and resid 5 through 12 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 46 through 47 current: chain 'P' and resid 82 through 86 Processing sheet with id=AC9, first strand: chain 'P' and resid 21 through 27 removed outlier: 3.524A pdb=" N LEU P 23 " --> pdb=" O SER P 119 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ASP P 121 " --> pdb=" O LEU P 23 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL P 25 " --> pdb=" O ASP P 121 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N VAL P 102 " --> pdb=" O MET P 115 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS P 117 " --> pdb=" O GLY P 100 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLY P 100 " --> pdb=" O LYS P 117 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER P 119 " --> pdb=" O VAL P 98 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL P 98 " --> pdb=" O SER P 119 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASP P 121 " --> pdb=" O GLY P 96 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLY P 96 " --> pdb=" O ASP P 121 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE P 59 " --> pdb=" O ASP P 71 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP P 71 " --> pdb=" O ILE P 59 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Q' and resid 5 through 12 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 46 through 47 current: chain 'Q' and resid 82 through 86 Processing sheet with id=AD2, first strand: chain 'Q' and resid 21 through 27 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 21 through 27 current: chain 'Q' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 68 through 72 current: chain 'Q' and resid 112 through 114 No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'R' and resid 23 through 26 removed outlier: 3.512A pdb=" N THR R 42 " --> pdb=" O ASN R 24 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA R 26 " --> pdb=" O ASN R 40 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'R' and resid 55 through 60 removed outlier: 3.817A pdb=" N ALA R 105 " --> pdb=" O ASP R 56 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'S' and resid 5 through 12 removed outlier: 6.744A pdb=" N VAL S 82 " --> pdb=" O GLU S 76 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'S' and resid 21 through 28 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 21 through 28 current: chain 'S' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 68 through 72 current: chain 'S' and resid 112 through 114 No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'T' and resid 5 through 12 removed outlier: 3.505A pdb=" N SER T 9 " --> pdb=" O GLN T 38 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 46 through 47 current: chain 'T' and resid 82 through 86 Processing sheet with id=AD8, first strand: chain 'T' and resid 21 through 27 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 21 through 27 current: chain 'T' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 68 through 72 current: chain 'T' and resid 112 through 114 No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'U' and resid 23 through 27 Processing sheet with id=AE1, first strand: chain 'U' and resid 55 through 60 removed outlier: 3.834A pdb=" N ALA U 105 " --> pdb=" O ASP U 56 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG U 116 " --> pdb=" O VAL U 102 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'V' and resid 5 through 12 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 46 through 47 current: chain 'V' and resid 82 through 86 Processing sheet with id=AE3, first strand: chain 'V' and resid 21 through 27 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 21 through 27 current: chain 'V' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 68 through 72 current: chain 'V' and resid 112 through 114 No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'W' and resid 5 through 12 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 46 through 47 current: chain 'W' and resid 82 through 86 Processing sheet with id=AE5, first strand: chain 'W' and resid 21 through 27 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 21 through 27 current: chain 'W' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 68 through 72 current: chain 'W' and resid 112 through 114 No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'X' and resid 23 through 26 removed outlier: 3.528A pdb=" N THR X 42 " --> pdb=" O ASN X 24 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA X 26 " --> pdb=" O ASN X 40 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'X' and resid 58 through 60 Processing sheet with id=AE8, first strand: chain 'Y' and resid 5 through 12 removed outlier: 6.732A pdb=" N VAL Y 82 " --> pdb=" O GLU Y 76 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Y' and resid 21 through 27 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 21 through 27 current: chain 'Y' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 68 through 72 current: chain 'Y' and resid 112 through 114 No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'Z' and resid 5 through 12 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 46 through 47 current: chain 'Z' and resid 82 through 86 Processing sheet with id=AF2, first strand: chain 'Z' and resid 21 through 27 removed outlier: 3.861A pdb=" N SER Z 21 " --> pdb=" O LYS Z 117 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ASP Z 121 " --> pdb=" O LEU Z 23 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL Z 25 " --> pdb=" O ASP Z 121 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR Z 112 " --> pdb=" O VAL Z 106 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL Z 106 " --> pdb=" O THR Z 112 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N VAL Z 114 " --> pdb=" O ILE Z 104 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE Z 104 " --> pdb=" O VAL Z 114 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ARG Z 116 " --> pdb=" O VAL Z 102 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL Z 102 " --> pdb=" O ARG Z 116 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR Z 138 " --> pdb=" O ARG Z 68 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN Z 70 " --> pdb=" O TYR Z 138 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'a' and resid 23 through 27 Processing sheet with id=AF4, first strand: chain 'a' and resid 55 through 60 removed outlier: 3.778A pdb=" N ALA a 105 " --> pdb=" O ASP a 56 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'b' and resid 5 through 12 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 46 through 47 current: chain 'b' and resid 82 through 86 Processing sheet with id=AF6, first strand: chain 'b' and resid 21 through 27 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 21 through 27 current: chain 'b' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 68 through 72 current: chain 'b' and resid 112 through 114 No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'c' and resid 5 through 12 removed outlier: 6.193A pdb=" N LYS c 5 " --> pdb=" O ILE c 36 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N GLN c 38 " --> pdb=" O LYS c 5 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N SER c 7 " --> pdb=" O GLN c 38 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ASN c 40 " --> pdb=" O SER c 7 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N SER c 9 " --> pdb=" O ASN c 40 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N THR c 42 " --> pdb=" O SER c 9 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N MET c 11 " --> pdb=" O THR c 42 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 46 through 47 current: chain 'c' and resid 82 through 86 Processing sheet with id=AF8, first strand: chain 'c' and resid 21 through 27 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 21 through 27 current: chain 'c' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 68 through 72 current: chain 'c' and resid 112 through 114 No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'd' and resid 23 through 26 removed outlier: 3.537A pdb=" N THR d 42 " --> pdb=" O ASN d 24 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA d 26 " --> pdb=" O ASN d 40 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'd' and resid 58 through 60 Processing sheet with id=AG2, first strand: chain 'e' and resid 5 through 12 WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 46 through 47 current: chain 'e' and resid 82 through 86 Processing sheet with id=AG3, first strand: chain 'e' and resid 21 through 27 WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 21 through 27 current: chain 'e' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 68 through 72 current: chain 'e' and resid 112 through 114 No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'f' and resid 5 through 12 removed outlier: 6.248A pdb=" N LYS f 5 " --> pdb=" O ILE f 36 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N GLN f 38 " --> pdb=" O LYS f 5 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N SER f 7 " --> pdb=" O GLN f 38 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ASN f 40 " --> pdb=" O SER f 7 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N SER f 9 " --> pdb=" O ASN f 40 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N THR f 42 " --> pdb=" O SER f 9 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N MET f 11 " --> pdb=" O THR f 42 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 46 through 47 current: chain 'f' and resid 82 through 86 Processing sheet with id=AG5, first strand: chain 'f' and resid 21 through 27 WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 21 through 27 current: chain 'f' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 68 through 72 current: chain 'f' and resid 112 through 114 No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'g' and resid 23 through 27 Processing sheet with id=AG7, first strand: chain 'g' and resid 55 through 60 removed outlier: 3.976A pdb=" N ALA g 105 " --> pdb=" O ASP g 56 " (cutoff:3.500A) 1055 hydrogen bonds defined for protein. 2775 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.76 Time building geometry restraints manager: 4.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 7050 1.28 - 1.41: 9379 1.41 - 1.55: 24138 1.55 - 1.68: 18 1.68 - 1.81: 214 Bond restraints: 40799 Sorted by residual: bond pdb=" CA ASP L 26 " pdb=" C ASP L 26 " ideal model delta sigma weight residual 1.529 1.434 0.095 9.30e-03 1.16e+04 1.05e+02 bond pdb=" CA PRO L 144 " pdb=" CB PRO L 144 " ideal model delta sigma weight residual 1.532 1.438 0.094 1.26e-02 6.30e+03 5.59e+01 bond pdb=" C PHE L 24 " pdb=" O PHE L 24 " ideal model delta sigma weight residual 1.235 1.153 0.082 1.12e-02 7.97e+03 5.38e+01 bond pdb=" CA SER L 142 " pdb=" C SER L 142 " ideal model delta sigma weight residual 1.521 1.425 0.096 1.36e-02 5.41e+03 4.98e+01 bond pdb=" C THR L 39 " pdb=" O THR L 39 " ideal model delta sigma weight residual 1.234 1.149 0.085 1.22e-02 6.72e+03 4.90e+01 ... (remaining 40794 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 54340 2.33 - 4.66: 570 4.66 - 6.98: 127 6.98 - 9.31: 33 9.31 - 11.64: 12 Bond angle restraints: 55082 Sorted by residual: angle pdb=" N GLU e 154 " pdb=" CA GLU e 154 " pdb=" C GLU e 154 " ideal model delta sigma weight residual 111.28 122.92 -11.64 1.09e+00 8.42e-01 1.14e+02 angle pdb=" N GLU L 35 " pdb=" CA GLU L 35 " pdb=" C GLU L 35 " ideal model delta sigma weight residual 111.28 122.12 -10.84 1.09e+00 8.42e-01 9.88e+01 angle pdb=" C VAL e 153 " pdb=" N GLU e 154 " pdb=" CA GLU e 154 " ideal model delta sigma weight residual 120.28 131.47 -11.19 1.34e+00 5.57e-01 6.97e+01 angle pdb=" N GLU Y 154 " pdb=" CA GLU Y 154 " pdb=" C GLU Y 154 " ideal model delta sigma weight residual 111.02 120.44 -9.42 1.22e+00 6.72e-01 5.96e+01 angle pdb=" N ASP L 32 " pdb=" CA ASP L 32 " pdb=" C ASP L 32 " ideal model delta sigma weight residual 111.36 119.64 -8.28 1.09e+00 8.42e-01 5.77e+01 ... (remaining 55077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 22484 17.95 - 35.91: 1930 35.91 - 53.86: 322 53.86 - 71.81: 67 71.81 - 89.76: 27 Dihedral angle restraints: 24830 sinusoidal: 9928 harmonic: 14902 Sorted by residual: dihedral pdb=" C LEU d 50 " pdb=" N LEU d 50 " pdb=" CA LEU d 50 " pdb=" CB LEU d 50 " ideal model delta harmonic sigma weight residual -122.60 -139.07 16.47 0 2.50e+00 1.60e-01 4.34e+01 dihedral pdb=" C LEU X 50 " pdb=" N LEU X 50 " pdb=" CA LEU X 50 " pdb=" CB LEU X 50 " ideal model delta harmonic sigma weight residual -122.60 -138.76 16.16 0 2.50e+00 1.60e-01 4.18e+01 dihedral pdb=" C LEU R 50 " pdb=" N LEU R 50 " pdb=" CA LEU R 50 " pdb=" CB LEU R 50 " ideal model delta harmonic sigma weight residual -122.60 -138.52 15.92 0 2.50e+00 1.60e-01 4.06e+01 ... (remaining 24827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 6317 0.144 - 0.288: 44 0.288 - 0.433: 16 0.433 - 0.577: 4 0.577 - 0.721: 5 Chirality restraints: 6386 Sorted by residual: chirality pdb=" CA LEU R 50 " pdb=" N LEU R 50 " pdb=" C LEU R 50 " pdb=" CB LEU R 50 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" CA LEU d 50 " pdb=" N LEU d 50 " pdb=" C LEU d 50 " pdb=" CB LEU d 50 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" CA LEU X 50 " pdb=" N LEU X 50 " pdb=" C LEU X 50 " pdb=" CB LEU X 50 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.22e+01 ... (remaining 6383 not shown) Planarity restraints: 7043 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN Y 151 " 0.022 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C GLN Y 151 " -0.072 2.00e-02 2.50e+03 pdb=" O GLN Y 151 " 0.025 2.00e-02 2.50e+03 pdb=" N ARG Y 152 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 50 " 0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C LEU R 50 " -0.061 2.00e-02 2.50e+03 pdb=" O LEU R 50 " 0.023 2.00e-02 2.50e+03 pdb=" N GLY R 51 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU d 50 " 0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C LEU d 50 " -0.060 2.00e-02 2.50e+03 pdb=" O LEU d 50 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY d 51 " 0.021 2.00e-02 2.50e+03 ... (remaining 7040 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 5945 2.77 - 3.30: 33400 3.30 - 3.83: 57589 3.83 - 4.37: 64138 4.37 - 4.90: 119562 Nonbonded interactions: 280634 Sorted by model distance: nonbonded pdb=" OD2 ASP U 31 " pdb=" OG1 THR U 34 " model vdw 2.233 3.040 nonbonded pdb=" OE2 GLU B 89 " pdb=" OH TYR B 111 " model vdw 2.272 3.040 nonbonded pdb=" OG1 THR f 14 " pdb=" OD1 ASP f 16 " model vdw 2.273 3.040 nonbonded pdb=" OD2 ASP S 143 " pdb=" OH TYR U 58 " model vdw 2.275 3.040 nonbonded pdb=" OG1 THR L 172 " pdb=" O VAL L 202 " model vdw 2.285 3.040 ... (remaining 280629 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 144 or resid 146 through 165)) selection = (chain 'B' and (resid 3 through 144 or resid 146 through 165)) selection = (chain 'C' and resid 3 through 165) selection = (chain 'D' and (resid 3 through 144 or resid 146 through 165)) selection = (chain 'E' and (resid 3 through 144 or resid 146 through 165)) selection = (chain 'F' and (resid 3 through 144 or resid 146 through 165)) } ncs_group { reference = (chain 'G' and resid 2 through 251) selection = (chain 'H' and resid 2 through 251) selection = (chain 'I' and resid 2 through 251) selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = (chain 'M' and resid 648 through 673) selection = (chain 'N' and resid 648 through 673) selection = chain 'O' } ncs_group { reference = chain 'P' selection = (chain 'Q' and resid 3 through 158) selection = chain 'S' selection = (chain 'T' and resid 3 through 158) selection = chain 'V' selection = (chain 'W' and resid 3 through 158) selection = chain 'Y' selection = (chain 'Z' and resid 3 through 158) selection = chain 'b' selection = (chain 'c' and resid 3 through 158) selection = chain 'e' selection = (chain 'f' and resid 3 through 158) } ncs_group { reference = chain 'R' selection = chain 'U' selection = chain 'X' selection = chain 'a' selection = chain 'd' selection = chain 'g' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 34.080 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.110 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 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 0.102 40799 Z= 0.335 Angle : 0.677 11.639 55082 Z= 0.422 Chirality : 0.056 0.721 6386 Planarity : 0.003 0.069 7043 Dihedral : 13.867 89.763 15188 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.49 % Favored : 97.21 % Rotamer: Outliers : 0.54 % Allowed : 0.49 % Favored : 98.97 % Cbeta Deviations : 0.33 % 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: -0.04 (0.12), residues: 4978 helix: 2.58 (0.21), residues: 654 sheet: 0.22 (0.13), residues: 1768 loop : -0.90 (0.12), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 152 TYR 0.030 0.001 TYR L 25 PHE 0.042 0.001 PHE L 24 TRP 0.008 0.001 TRP D 91 HIS 0.007 0.001 HIS b 63 Details of bonding type rmsd covalent geometry : bond 0.00509 (40799) covalent geometry : angle 0.67670 (55082) hydrogen bonds : bond 0.23287 ( 1055) hydrogen bonds : angle 7.16502 ( 2775) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 4471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 698 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 29 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8434 (tt) REVERT: M 671 ASN cc_start: 0.8562 (m110) cc_final: 0.8324 (m110) REVERT: P 141 THR cc_start: 0.8685 (t) cc_final: 0.8290 (p) REVERT: R 24 ASN cc_start: 0.8680 (t0) cc_final: 0.8395 (t0) REVERT: R 29 ASN cc_start: 0.7676 (m110) cc_final: 0.7320 (m-40) REVERT: R 111 ASP cc_start: 0.8798 (p0) cc_final: 0.8369 (p0) REVERT: X 24 ASN cc_start: 0.8966 (t0) cc_final: 0.8675 (t0) REVERT: Y 152 ARG cc_start: 0.7790 (ttm170) cc_final: 0.7575 (ttp-170) REVERT: a 117 LYS cc_start: 0.8242 (mtmm) cc_final: 0.8039 (mttp) REVERT: b 115 MET cc_start: 0.8048 (mmm) cc_final: 0.7838 (mtm) REVERT: d 29 ASN cc_start: 0.8134 (m110) cc_final: 0.7930 (m110) REVERT: d 115 MET cc_start: 0.8150 (ttt) cc_final: 0.7875 (ttt) REVERT: f 127 MET cc_start: 0.8046 (tpt) cc_final: 0.7842 (tpp) REVERT: g 58 TYR cc_start: 0.8081 (t80) cc_final: 0.7567 (t80) outliers start: 24 outliers final: 14 residues processed: 717 average time/residue: 0.2371 time to fit residues: 276.0390 Evaluate side-chains 625 residues out of total 4471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 610 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 153 SER Chi-restraints excluded: chain L residue 26 ASP Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 31 GLU Chi-restraints excluded: chain L residue 145 TYR Chi-restraints excluded: chain L residue 153 SER Chi-restraints excluded: chain P residue 151 GLN Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 156 ILE Chi-restraints excluded: chain Y residue 156 ILE Chi-restraints excluded: chain d residue 134 VAL Chi-restraints excluded: chain e residue 156 ILE Chi-restraints excluded: chain g residue 135 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 8.9990 chunk 455 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 470 optimal weight: 6.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 163 GLN P 29 ASN P 70 GLN P 151 GLN R 54 ASN T 29 ASN T 84 GLN U 29 ASN W 24 ASN X 30 GLN X 54 ASN Y 24 ASN Y 70 GLN Z 29 ASN b 70 GLN c 29 ASN d 54 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.101752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.079449 restraints weight = 72205.029| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.38 r_work: 0.2849 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 40799 Z= 0.151 Angle : 0.508 8.448 55082 Z= 0.279 Chirality : 0.047 0.164 6386 Planarity : 0.003 0.060 7043 Dihedral : 5.028 57.737 5453 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.13 % Favored : 96.69 % Rotamer: Outliers : 1.07 % Allowed : 6.22 % Favored : 92.71 % 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: 0.07 (0.12), residues: 4978 helix: 2.58 (0.21), residues: 678 sheet: 0.39 (0.13), residues: 1786 loop : -0.92 (0.12), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 71 TYR 0.019 0.001 TYR X 28 PHE 0.014 0.001 PHE C 112 TRP 0.009 0.001 TRP D 91 HIS 0.003 0.001 HIS E 74 Details of bonding type rmsd covalent geometry : bond 0.00359 (40799) covalent geometry : angle 0.50766 (55082) hydrogen bonds : bond 0.04764 ( 1055) hydrogen bonds : angle 5.21443 ( 2775) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 4471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 627 time to evaluate : 1.693 Fit side-chains REVERT: D 59 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8498 (pt0) REVERT: G 95 MET cc_start: 0.9505 (mmm) cc_final: 0.8738 (tpt) REVERT: G 218 ARG cc_start: 0.9048 (mmt90) cc_final: 0.8755 (mtp85) REVERT: J 47 MET cc_start: 0.8604 (mmm) cc_final: 0.8363 (mmm) REVERT: L 102 GLU cc_start: 0.8526 (pm20) cc_final: 0.8124 (pt0) REVERT: M 671 ASN cc_start: 0.8526 (m110) cc_final: 0.8234 (m110) REVERT: P 141 THR cc_start: 0.8493 (t) cc_final: 0.8053 (p) REVERT: R 24 ASN cc_start: 0.8563 (t0) cc_final: 0.8337 (t0) REVERT: S 45 ASP cc_start: 0.8570 (t0) cc_final: 0.8321 (t0) REVERT: T 79 GLU cc_start: 0.8669 (tp30) cc_final: 0.8291 (tp30) REVERT: U 115 MET cc_start: 0.8607 (ttm) cc_final: 0.7991 (ttm) REVERT: U 117 LYS cc_start: 0.7873 (mtmm) cc_final: 0.7578 (mttp) REVERT: V 17 TYR cc_start: 0.8757 (t80) cc_final: 0.8490 (t80) REVERT: V 79 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8345 (tm-30) REVERT: X 24 ASN cc_start: 0.8875 (t0) cc_final: 0.8401 (t0) REVERT: Y 45 ASP cc_start: 0.8732 (t0) cc_final: 0.8431 (t0) REVERT: Z 68 ARG cc_start: 0.9025 (ttm170) cc_final: 0.8793 (ttm170) REVERT: Z 79 GLU cc_start: 0.8490 (tp30) cc_final: 0.8226 (tp30) REVERT: a 117 LYS cc_start: 0.7917 (mtmm) cc_final: 0.7702 (mttp) REVERT: c 24 ASN cc_start: 0.8817 (t0) cc_final: 0.8464 (t0) REVERT: f 76 GLU cc_start: 0.8558 (tp30) cc_final: 0.8233 (tm-30) REVERT: f 79 GLU cc_start: 0.8685 (tp30) cc_final: 0.8372 (tp30) REVERT: f 127 MET cc_start: 0.8883 (tpt) cc_final: 0.8593 (tpp) REVERT: f 145 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8542 (tt) REVERT: f 154 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7844 (mm-30) REVERT: g 115 MET cc_start: 0.8433 (ttp) cc_final: 0.8120 (ttt) outliers start: 48 outliers final: 37 residues processed: 657 average time/residue: 0.2418 time to fit residues: 258.3490 Evaluate side-chains 622 residues out of total 4471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 584 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain L residue 26 ASP Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain N residue 659 ASP Chi-restraints excluded: chain N residue 670 ILE Chi-restraints excluded: chain O residue 670 ILE Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain P residue 131 SER Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain R residue 22 ASP Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain U residue 36 ILE Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain U residue 134 VAL Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain V residue 136 LEU Chi-restraints excluded: chain V residue 147 THR Chi-restraints excluded: chain W residue 53 SER Chi-restraints excluded: chain W residue 147 THR Chi-restraints excluded: chain Y residue 156 ILE Chi-restraints excluded: chain b residue 11 MET Chi-restraints excluded: chain b residue 156 ILE Chi-restraints excluded: chain c residue 42 THR Chi-restraints excluded: chain c residue 147 THR Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain e residue 156 ILE Chi-restraints excluded: chain f residue 141 THR Chi-restraints excluded: chain f residue 144 ASP Chi-restraints excluded: chain f residue 145 LEU Chi-restraints excluded: chain g residue 135 LYS Chi-restraints excluded: chain g residue 160 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 451 optimal weight: 5.9990 chunk 180 optimal weight: 0.9990 chunk 490 optimal weight: 3.9990 chunk 479 optimal weight: 9.9990 chunk 436 optimal weight: 8.9990 chunk 270 optimal weight: 4.9990 chunk 446 optimal weight: 10.0000 chunk 478 optimal weight: 0.9990 chunk 399 optimal weight: 0.0570 chunk 192 optimal weight: 5.9990 chunk 376 optimal weight: 6.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 GLN R 30 GLN U 29 ASN V 30 GLN W 24 ASN X 54 ASN Y 38 GLN d 30 GLN d 54 ASN e 24 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.101498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.079243 restraints weight = 71880.210| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.37 r_work: 0.2846 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 40799 Z= 0.142 Angle : 0.483 8.203 55082 Z= 0.266 Chirality : 0.046 0.163 6386 Planarity : 0.002 0.054 7043 Dihedral : 4.708 58.493 5437 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.85 % Favored : 97.01 % Rotamer: Outliers : 1.68 % Allowed : 7.90 % Favored : 90.43 % 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: 0.10 (0.12), residues: 4978 helix: 2.63 (0.21), residues: 679 sheet: 0.39 (0.13), residues: 1786 loop : -0.91 (0.12), residues: 2513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG b 109 TYR 0.019 0.001 TYR X 28 PHE 0.013 0.001 PHE C 112 TRP 0.008 0.001 TRP D 91 HIS 0.003 0.001 HIS E 74 Details of bonding type rmsd covalent geometry : bond 0.00339 (40799) covalent geometry : angle 0.48277 (55082) hydrogen bonds : bond 0.04255 ( 1055) hydrogen bonds : angle 4.79610 ( 2775) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 4471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 600 time to evaluate : 1.732 Fit side-chains REVERT: D 59 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8485 (pt0) REVERT: G 95 MET cc_start: 0.9486 (mmm) cc_final: 0.8791 (tpt) REVERT: G 166 MET cc_start: 0.8917 (tpp) cc_final: 0.8685 (tpt) REVERT: G 218 ARG cc_start: 0.9039 (mmt90) cc_final: 0.8725 (mtp85) REVERT: J 95 MET cc_start: 0.9075 (tpp) cc_final: 0.8599 (tpp) REVERT: L 29 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7553 (tt) REVERT: L 102 GLU cc_start: 0.8566 (pm20) cc_final: 0.8132 (pt0) REVERT: M 671 ASN cc_start: 0.8501 (m110) cc_final: 0.8261 (m110) REVERT: P 149 ILE cc_start: 0.7616 (tp) cc_final: 0.7363 (tt) REVERT: Q 152 ARG cc_start: 0.7814 (mtp180) cc_final: 0.7569 (ttm170) REVERT: R 24 ASN cc_start: 0.8499 (t0) cc_final: 0.8266 (t0) REVERT: R 28 TYR cc_start: 0.8724 (t80) cc_final: 0.8297 (t80) REVERT: R 29 ASN cc_start: 0.8175 (m-40) cc_final: 0.7636 (m110) REVERT: S 45 ASP cc_start: 0.8607 (t0) cc_final: 0.8368 (t0) REVERT: S 76 GLU cc_start: 0.8812 (tp30) cc_final: 0.8521 (tp30) REVERT: T 79 GLU cc_start: 0.8654 (tp30) cc_final: 0.8268 (tp30) REVERT: U 29 ASN cc_start: 0.8945 (OUTLIER) cc_final: 0.8700 (t0) REVERT: V 17 TYR cc_start: 0.8788 (t80) cc_final: 0.8503 (t80) REVERT: X 24 ASN cc_start: 0.8828 (t0) cc_final: 0.8301 (t0) REVERT: Y 45 ASP cc_start: 0.8734 (t0) cc_final: 0.8487 (t0) REVERT: d 24 ASN cc_start: 0.8391 (t0) cc_final: 0.7902 (t0) REVERT: d 28 TYR cc_start: 0.8754 (t80) cc_final: 0.8453 (t80) REVERT: f 76 GLU cc_start: 0.8583 (tp30) cc_final: 0.8250 (tm-30) REVERT: f 79 GLU cc_start: 0.8668 (tp30) cc_final: 0.8351 (tp30) REVERT: f 127 MET cc_start: 0.8866 (tpt) cc_final: 0.8550 (tpp) REVERT: f 154 GLU cc_start: 0.8295 (mm-30) cc_final: 0.8045 (mm-30) outliers start: 75 outliers final: 52 residues processed: 641 average time/residue: 0.2295 time to fit residues: 239.3225 Evaluate side-chains 637 residues out of total 4471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 583 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain B residue 28 MET Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 95 MET Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain N residue 670 ILE Chi-restraints excluded: chain O residue 670 ILE Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain P residue 131 SER Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain R residue 22 ASP Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 42 THR Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain V residue 147 THR Chi-restraints excluded: chain W residue 42 THR Chi-restraints excluded: chain W residue 147 THR Chi-restraints excluded: chain X residue 36 ILE Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain Y residue 156 ILE Chi-restraints excluded: chain Z residue 141 THR Chi-restraints excluded: chain a residue 50 LEU Chi-restraints excluded: chain a residue 160 ILE Chi-restraints excluded: chain b residue 11 MET Chi-restraints excluded: chain b residue 147 THR Chi-restraints excluded: chain c residue 42 THR Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 111 ASP Chi-restraints excluded: chain e residue 147 THR Chi-restraints excluded: chain f residue 144 ASP Chi-restraints excluded: chain g residue 36 ILE Chi-restraints excluded: chain g residue 135 LYS Chi-restraints excluded: chain g residue 160 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 92 optimal weight: 8.9990 chunk 307 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 407 optimal weight: 7.9990 chunk 477 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 277 optimal weight: 3.9990 chunk 448 optimal weight: 5.9990 chunk 234 optimal weight: 5.9990 chunk 391 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 54 ASN W 24 ASN X 54 ASN d 54 ASN e 24 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.100964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.079730 restraints weight = 72487.691| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.21 r_work: 0.2865 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 40799 Z= 0.192 Angle : 0.515 8.229 55082 Z= 0.283 Chirality : 0.047 0.173 6386 Planarity : 0.003 0.052 7043 Dihedral : 4.750 57.790 5431 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.66 % Favored : 96.22 % Rotamer: Outliers : 2.08 % Allowed : 8.81 % Favored : 89.11 % 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: -0.02 (0.12), residues: 4978 helix: 2.53 (0.21), residues: 679 sheet: 0.30 (0.13), residues: 1783 loop : -0.97 (0.12), residues: 2516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 71 TYR 0.020 0.001 TYR g 28 PHE 0.015 0.002 PHE C 112 TRP 0.008 0.001 TRP D 91 HIS 0.004 0.001 HIS E 74 Details of bonding type rmsd covalent geometry : bond 0.00470 (40799) covalent geometry : angle 0.51474 (55082) hydrogen bonds : bond 0.04654 ( 1055) hydrogen bonds : angle 4.73516 ( 2775) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 4471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 577 time to evaluate : 1.310 Fit side-chains revert: symmetry clash REVERT: D 59 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8489 (pt0) REVERT: G 95 MET cc_start: 0.9528 (mmm) cc_final: 0.8955 (tpt) REVERT: G 218 ARG cc_start: 0.8988 (mmt90) cc_final: 0.8702 (mtp85) REVERT: I 95 MET cc_start: 0.9432 (mmm) cc_final: 0.8856 (tpt) REVERT: J 95 MET cc_start: 0.9129 (tpp) cc_final: 0.8837 (tpp) REVERT: L 102 GLU cc_start: 0.8524 (pm20) cc_final: 0.8103 (pt0) REVERT: M 671 ASN cc_start: 0.8630 (m110) cc_final: 0.8368 (m110) REVERT: P 149 ILE cc_start: 0.7964 (tp) cc_final: 0.7611 (tt) REVERT: R 24 ASN cc_start: 0.8619 (t0) cc_final: 0.8414 (t0) REVERT: S 45 ASP cc_start: 0.8518 (t0) cc_final: 0.8195 (t0) REVERT: S 76 GLU cc_start: 0.8783 (tp30) cc_final: 0.8543 (tp30) REVERT: T 79 GLU cc_start: 0.8239 (tp30) cc_final: 0.7906 (tp30) REVERT: X 24 ASN cc_start: 0.8962 (t0) cc_final: 0.8385 (t0) REVERT: Y 45 ASP cc_start: 0.8739 (t0) cc_final: 0.8419 (t0) REVERT: Y 54 ASN cc_start: 0.7621 (t0) cc_final: 0.7372 (t0) REVERT: Y 130 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.8425 (m-80) REVERT: a 157 GLU cc_start: 0.7012 (pp20) cc_final: 0.6715 (pp20) REVERT: d 24 ASN cc_start: 0.8480 (t0) cc_final: 0.8040 (t0) REVERT: d 28 TYR cc_start: 0.8832 (t80) cc_final: 0.8534 (t80) REVERT: f 76 GLU cc_start: 0.8581 (tp30) cc_final: 0.8311 (tm-30) REVERT: f 79 GLU cc_start: 0.8530 (tp30) cc_final: 0.8229 (tp30) REVERT: f 127 MET cc_start: 0.8829 (tpt) cc_final: 0.8608 (tpp) REVERT: f 154 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7777 (mm-30) REVERT: g 22 ASP cc_start: 0.8736 (p0) cc_final: 0.8462 (p0) outliers start: 93 outliers final: 76 residues processed: 627 average time/residue: 0.2271 time to fit residues: 230.3650 Evaluate side-chains 638 residues out of total 4471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 561 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain B residue 28 MET Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain L residue 95 MET Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain N residue 670 ILE Chi-restraints excluded: chain O residue 659 ASP Chi-restraints excluded: chain O residue 670 ILE Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain P residue 131 SER Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 147 THR Chi-restraints excluded: chain R residue 22 ASP Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain T residue 130 PHE Chi-restraints excluded: chain U residue 42 THR Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain U residue 136 LEU Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain U residue 156 ILE Chi-restraints excluded: chain V residue 147 THR Chi-restraints excluded: chain W residue 42 THR Chi-restraints excluded: chain W residue 147 THR Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain X residue 36 ILE Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 111 ASP Chi-restraints excluded: chain X residue 118 ILE Chi-restraints excluded: chain Y residue 84 GLN Chi-restraints excluded: chain Y residue 115 MET Chi-restraints excluded: chain Y residue 130 PHE Chi-restraints excluded: chain Y residue 150 LYS Chi-restraints excluded: chain Y residue 156 ILE Chi-restraints excluded: chain Z residue 25 VAL Chi-restraints excluded: chain Z residue 130 PHE Chi-restraints excluded: chain Z residue 141 THR Chi-restraints excluded: chain a residue 50 LEU Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 160 ILE Chi-restraints excluded: chain b residue 11 MET Chi-restraints excluded: chain b residue 147 THR Chi-restraints excluded: chain c residue 42 THR Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 147 THR Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain e residue 24 ASN Chi-restraints excluded: chain e residue 147 THR Chi-restraints excluded: chain f residue 141 THR Chi-restraints excluded: chain f residue 144 ASP Chi-restraints excluded: chain f residue 145 LEU Chi-restraints excluded: chain g residue 36 ILE Chi-restraints excluded: chain g residue 135 LYS Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 160 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 408 optimal weight: 4.9990 chunk 489 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 chunk 222 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 413 optimal weight: 8.9990 chunk 429 optimal weight: 7.9990 chunk 295 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 chunk 230 optimal weight: 2.9990 chunk 236 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 54 ASN W 24 ASN X 54 ASN d 54 ASN e 24 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.099452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.078308 restraints weight = 72729.442| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.20 r_work: 0.2840 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 40799 Z= 0.245 Angle : 0.555 8.205 55082 Z= 0.305 Chirality : 0.048 0.263 6386 Planarity : 0.003 0.051 7043 Dihedral : 4.960 57.807 5431 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.84 % Favored : 95.98 % Rotamer: Outliers : 2.33 % Allowed : 9.80 % Favored : 87.88 % 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: -0.20 (0.12), residues: 4978 helix: 2.34 (0.20), residues: 679 sheet: 0.12 (0.13), residues: 1786 loop : -1.02 (0.12), residues: 2513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 71 TYR 0.021 0.002 TYR g 28 PHE 0.018 0.002 PHE C 112 TRP 0.008 0.002 TRP D 91 HIS 0.005 0.001 HIS E 74 Details of bonding type rmsd covalent geometry : bond 0.00603 (40799) covalent geometry : angle 0.55524 (55082) hydrogen bonds : bond 0.05139 ( 1055) hydrogen bonds : angle 4.81663 ( 2775) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 4471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 563 time to evaluate : 1.261 Fit side-chains REVERT: D 59 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8580 (pt0) REVERT: G 95 MET cc_start: 0.9531 (mmm) cc_final: 0.8957 (tpt) REVERT: G 218 ARG cc_start: 0.8992 (mmt90) cc_final: 0.8706 (mtp85) REVERT: H 95 MET cc_start: 0.9313 (mmm) cc_final: 0.8935 (tpt) REVERT: I 95 MET cc_start: 0.9442 (mmm) cc_final: 0.8857 (tpt) REVERT: L 29 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8049 (tt) REVERT: L 102 GLU cc_start: 0.8538 (pm20) cc_final: 0.8117 (pt0) REVERT: M 671 ASN cc_start: 0.8877 (m110) cc_final: 0.8576 (m110) REVERT: P 50 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8272 (mm) REVERT: R 24 ASN cc_start: 0.8682 (t0) cc_final: 0.8438 (t0) REVERT: R 29 ASN cc_start: 0.8010 (m-40) cc_final: 0.7662 (m-40) REVERT: S 45 ASP cc_start: 0.8512 (t0) cc_final: 0.8234 (t0) REVERT: S 152 ARG cc_start: 0.7996 (ttp-170) cc_final: 0.7661 (ttm170) REVERT: U 43 ARG cc_start: 0.7907 (ttt180) cc_final: 0.7706 (ttt180) REVERT: V 71 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8447 (m-30) REVERT: X 24 ASN cc_start: 0.8994 (t0) cc_final: 0.8577 (t0) REVERT: Y 45 ASP cc_start: 0.8752 (t0) cc_final: 0.8528 (t0) REVERT: Y 50 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7948 (mm) REVERT: Y 130 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8494 (m-80) REVERT: d 24 ASN cc_start: 0.8498 (t0) cc_final: 0.8085 (t0) REVERT: d 28 TYR cc_start: 0.8842 (t80) cc_final: 0.8487 (t80) REVERT: f 76 GLU cc_start: 0.8615 (tp30) cc_final: 0.8356 (tm-30) REVERT: f 79 GLU cc_start: 0.8544 (tp30) cc_final: 0.8209 (tp30) REVERT: f 145 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8327 (tp) REVERT: f 154 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7874 (mm-30) REVERT: g 22 ASP cc_start: 0.8840 (p0) cc_final: 0.8575 (p0) outliers start: 104 outliers final: 78 residues processed: 627 average time/residue: 0.2353 time to fit residues: 238.7052 Evaluate side-chains 639 residues out of total 4471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 555 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain B residue 28 MET Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain N residue 670 ILE Chi-restraints excluded: chain O residue 659 ASP Chi-restraints excluded: chain O residue 670 ILE Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain P residue 131 SER Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 147 THR Chi-restraints excluded: chain R residue 22 ASP Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 144 ASP Chi-restraints excluded: chain T residue 128 THR Chi-restraints excluded: chain T residue 130 PHE Chi-restraints excluded: chain U residue 36 ILE Chi-restraints excluded: chain U residue 42 THR Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain U residue 136 LEU Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain U residue 156 ILE Chi-restraints excluded: chain V residue 71 ASP Chi-restraints excluded: chain V residue 136 LEU Chi-restraints excluded: chain V residue 147 THR Chi-restraints excluded: chain W residue 42 THR Chi-restraints excluded: chain W residue 147 THR Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 111 ASP Chi-restraints excluded: chain X residue 118 ILE Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 84 GLN Chi-restraints excluded: chain Y residue 115 MET Chi-restraints excluded: chain Y residue 130 PHE Chi-restraints excluded: chain Y residue 150 LYS Chi-restraints excluded: chain Y residue 156 ILE Chi-restraints excluded: chain Z residue 25 VAL Chi-restraints excluded: chain Z residue 130 PHE Chi-restraints excluded: chain Z residue 141 THR Chi-restraints excluded: chain a residue 50 LEU Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 160 ILE Chi-restraints excluded: chain b residue 11 MET Chi-restraints excluded: chain b residue 147 THR Chi-restraints excluded: chain c residue 42 THR Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 56 ASP Chi-restraints excluded: chain c residue 147 THR Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 111 ASP Chi-restraints excluded: chain e residue 147 THR Chi-restraints excluded: chain f residue 141 THR Chi-restraints excluded: chain f residue 144 ASP Chi-restraints excluded: chain f residue 145 LEU Chi-restraints excluded: chain g residue 36 ILE Chi-restraints excluded: chain g residue 50 LEU Chi-restraints excluded: chain g residue 135 LYS Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 160 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 479 optimal weight: 0.9990 chunk 223 optimal weight: 0.0060 chunk 101 optimal weight: 0.0370 chunk 396 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 chunk 400 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 85 optimal weight: 0.2980 chunk 328 optimal weight: 0.9990 chunk 165 optimal weight: 10.0000 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 24 ASN X 54 ASN b 30 GLN d 54 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.104683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.083633 restraints weight = 71816.590| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.19 r_work: 0.2937 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 40799 Z= 0.080 Angle : 0.449 8.139 55082 Z= 0.246 Chirality : 0.045 0.207 6386 Planarity : 0.002 0.049 7043 Dihedral : 4.311 56.376 5431 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.27 % Favored : 97.63 % Rotamer: Outliers : 1.27 % Allowed : 11.43 % Favored : 87.30 % 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: 0.18 (0.12), residues: 4978 helix: 2.72 (0.21), residues: 679 sheet: 0.39 (0.13), residues: 1773 loop : -0.81 (0.12), residues: 2526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG d 43 TYR 0.015 0.001 TYR g 28 PHE 0.027 0.001 PHE W 130 TRP 0.009 0.001 TRP D 91 HIS 0.002 0.000 HIS b 63 Details of bonding type rmsd covalent geometry : bond 0.00166 (40799) covalent geometry : angle 0.44910 (55082) hydrogen bonds : bond 0.02785 ( 1055) hydrogen bonds : angle 4.23708 ( 2775) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 4471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 614 time to evaluate : 1.149 Fit side-chains revert: symmetry clash REVERT: D 59 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8518 (pt0) REVERT: G 47 MET cc_start: 0.7078 (OUTLIER) cc_final: 0.4481 (ptm) REVERT: G 95 MET cc_start: 0.9416 (mmm) cc_final: 0.9127 (tpt) REVERT: G 218 ARG cc_start: 0.8850 (mmt90) cc_final: 0.8566 (mtp85) REVERT: J 2 TYR cc_start: 0.6138 (OUTLIER) cc_final: 0.5871 (m-80) REVERT: J 47 MET cc_start: 0.8398 (mmm) cc_final: 0.8150 (mmm) REVERT: L 29 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7558 (tt) REVERT: P 50 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8341 (mm) REVERT: P 52 LYS cc_start: 0.8750 (pptt) cc_final: 0.8486 (tppt) REVERT: R 24 ASN cc_start: 0.8598 (t0) cc_final: 0.8389 (t0) REVERT: S 45 ASP cc_start: 0.8524 (t0) cc_final: 0.8206 (t0) REVERT: T 78 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8402 (mt-10) REVERT: T 145 LEU cc_start: 0.8665 (tp) cc_final: 0.8465 (tt) REVERT: U 117 LYS cc_start: 0.7535 (mtmm) cc_final: 0.7328 (mttp) REVERT: V 79 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8277 (tm-30) REVERT: X 24 ASN cc_start: 0.8876 (t0) cc_final: 0.8403 (t0) REVERT: X 107 LYS cc_start: 0.9236 (mtpp) cc_final: 0.9012 (mttp) REVERT: Y 45 ASP cc_start: 0.8684 (t0) cc_final: 0.8444 (t0) REVERT: Y 50 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7419 (mm) REVERT: Y 115 MET cc_start: 0.9349 (mmt) cc_final: 0.8944 (mmp) REVERT: Y 130 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.8392 (m-80) REVERT: d 24 ASN cc_start: 0.8418 (t0) cc_final: 0.8002 (t0) REVERT: d 28 TYR cc_start: 0.8824 (t80) cc_final: 0.8447 (t80) REVERT: d 99 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7591 (mp) REVERT: f 76 GLU cc_start: 0.8512 (tp30) cc_final: 0.8287 (tm-30) REVERT: f 79 GLU cc_start: 0.8474 (tp30) cc_final: 0.8205 (tp30) REVERT: f 154 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7889 (mm-30) outliers start: 57 outliers final: 34 residues processed: 648 average time/residue: 0.2344 time to fit residues: 246.3849 Evaluate side-chains 623 residues out of total 4471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 582 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 MET Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain J residue 2 TYR Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain R residue 22 ASP Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 144 ASP Chi-restraints excluded: chain T residue 130 PHE Chi-restraints excluded: chain U residue 42 THR Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain W residue 53 SER Chi-restraints excluded: chain W residue 127 MET Chi-restraints excluded: chain X residue 111 ASP Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 130 PHE Chi-restraints excluded: chain Y residue 156 ILE Chi-restraints excluded: chain Z residue 130 PHE Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 160 ILE Chi-restraints excluded: chain b residue 11 MET Chi-restraints excluded: chain b residue 50 LEU Chi-restraints excluded: chain b residue 71 ASP Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain f residue 145 LEU Chi-restraints excluded: chain g residue 135 LYS Chi-restraints excluded: chain g residue 160 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 321 optimal weight: 5.9990 chunk 190 optimal weight: 10.0000 chunk 256 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 270 optimal weight: 9.9990 chunk 347 optimal weight: 2.9990 chunk 266 optimal weight: 5.9990 chunk 474 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 298 optimal weight: 5.9990 chunk 449 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 163 GLN L 163 GLN W 24 ASN X 54 ASN d 54 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.099834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.078589 restraints weight = 72873.084| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.22 r_work: 0.2847 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 40799 Z= 0.235 Angle : 0.552 8.425 55082 Z= 0.301 Chirality : 0.048 0.173 6386 Planarity : 0.003 0.049 7043 Dihedral : 4.700 56.761 5428 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.24 % Favored : 95.64 % Rotamer: Outliers : 1.66 % Allowed : 11.74 % Favored : 86.60 % 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: -0.04 (0.12), residues: 4978 helix: 2.51 (0.20), residues: 679 sheet: 0.19 (0.13), residues: 1787 loop : -0.90 (0.12), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 71 TYR 0.020 0.002 TYR g 28 PHE 0.035 0.002 PHE g 142 TRP 0.008 0.002 TRP E 26 HIS 0.005 0.001 HIS E 74 Details of bonding type rmsd covalent geometry : bond 0.00576 (40799) covalent geometry : angle 0.55200 (55082) hydrogen bonds : bond 0.04813 ( 1055) hydrogen bonds : angle 4.59690 ( 2775) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 4471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 564 time to evaluate : 1.655 Fit side-chains revert: symmetry clash REVERT: D 59 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8559 (pt0) REVERT: G 95 MET cc_start: 0.9526 (mmm) cc_final: 0.8959 (tpt) REVERT: G 218 ARG cc_start: 0.8976 (mmt90) cc_final: 0.8679 (mtp85) REVERT: H 95 MET cc_start: 0.9340 (mmm) cc_final: 0.8959 (tpt) REVERT: L 29 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8058 (tt) REVERT: L 102 GLU cc_start: 0.8625 (pm20) cc_final: 0.8190 (pt0) REVERT: P 50 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8278 (mm) REVERT: R 24 ASN cc_start: 0.8666 (t0) cc_final: 0.8434 (t0) REVERT: R 28 TYR cc_start: 0.8654 (t80) cc_final: 0.8246 (t80) REVERT: S 45 ASP cc_start: 0.8518 (t0) cc_final: 0.8230 (t0) REVERT: S 50 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7998 (mm) REVERT: T 137 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7849 (mm-30) REVERT: X 24 ASN cc_start: 0.8944 (t0) cc_final: 0.8366 (t0) REVERT: X 38 GLN cc_start: 0.7587 (mp10) cc_final: 0.7193 (mp10) REVERT: Y 45 ASP cc_start: 0.8714 (t0) cc_final: 0.8470 (t0) REVERT: Y 50 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7776 (mm) REVERT: Y 130 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.8453 (m-80) REVERT: b 127 MET cc_start: 0.9131 (mmm) cc_final: 0.8891 (tpp) REVERT: d 24 ASN cc_start: 0.8451 (t0) cc_final: 0.8077 (t0) REVERT: d 28 TYR cc_start: 0.8849 (t80) cc_final: 0.8466 (t80) REVERT: f 11 MET cc_start: 0.8288 (mtm) cc_final: 0.8056 (mtp) REVERT: f 79 GLU cc_start: 0.8568 (tp30) cc_final: 0.8239 (tp30) REVERT: f 145 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8386 (tp) REVERT: f 154 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7923 (mm-30) REVERT: g 135 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8336 (ttmm) outliers start: 74 outliers final: 54 residues processed: 609 average time/residue: 0.2513 time to fit residues: 246.9989 Evaluate side-chains 609 residues out of total 4471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 548 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain B residue 28 MET Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain J residue 2 TYR Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain K residue 111 GLU Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain N residue 670 ILE Chi-restraints excluded: chain O residue 659 ASP Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain P residue 115 MET Chi-restraints excluded: chain R residue 22 ASP Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain T residue 130 PHE Chi-restraints excluded: chain U residue 42 THR Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 98 VAL Chi-restraints excluded: chain V residue 147 THR Chi-restraints excluded: chain X residue 111 ASP Chi-restraints excluded: chain X residue 118 ILE Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 84 GLN Chi-restraints excluded: chain Y residue 130 PHE Chi-restraints excluded: chain Y residue 150 LYS Chi-restraints excluded: chain Y residue 156 ILE Chi-restraints excluded: chain Z residue 25 VAL Chi-restraints excluded: chain Z residue 130 PHE Chi-restraints excluded: chain a residue 42 THR Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 160 ILE Chi-restraints excluded: chain b residue 50 LEU Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 111 ASP Chi-restraints excluded: chain f residue 144 ASP Chi-restraints excluded: chain f residue 145 LEU Chi-restraints excluded: chain g residue 135 LYS Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 160 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 11 optimal weight: 2.9990 chunk 281 optimal weight: 9.9990 chunk 298 optimal weight: 10.0000 chunk 208 optimal weight: 9.9990 chunk 435 optimal weight: 1.9990 chunk 360 optimal weight: 5.9990 chunk 488 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 63 optimal weight: 0.0970 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 163 GLN W 24 ASN X 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.101831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.080712 restraints weight = 72013.383| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.20 r_work: 0.2885 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 40799 Z= 0.124 Angle : 0.481 7.912 55082 Z= 0.264 Chirality : 0.046 0.164 6386 Planarity : 0.002 0.049 7043 Dihedral : 4.475 56.218 5428 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.83 % Favored : 97.05 % Rotamer: Outliers : 1.39 % Allowed : 12.28 % Favored : 86.33 % 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: 0.07 (0.12), residues: 4978 helix: 2.61 (0.21), residues: 679 sheet: 0.26 (0.13), residues: 1786 loop : -0.82 (0.12), residues: 2513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG U 152 TYR 0.017 0.001 TYR g 28 PHE 0.031 0.001 PHE g 142 TRP 0.009 0.001 TRP D 91 HIS 0.003 0.001 HIS D 74 Details of bonding type rmsd covalent geometry : bond 0.00292 (40799) covalent geometry : angle 0.48121 (55082) hydrogen bonds : bond 0.03678 ( 1055) hydrogen bonds : angle 4.35476 ( 2775) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 4471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 556 time to evaluate : 1.650 Fit side-chains revert: symmetry clash REVERT: D 59 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8475 (pt0) REVERT: G 95 MET cc_start: 0.9504 (mmm) cc_final: 0.8996 (tpt) REVERT: G 218 ARG cc_start: 0.8850 (mmt90) cc_final: 0.8558 (mtp85) REVERT: L 29 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7855 (tt) REVERT: L 102 GLU cc_start: 0.8410 (pm20) cc_final: 0.8004 (pt0) REVERT: P 50 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8346 (mm) REVERT: R 24 ASN cc_start: 0.8623 (t0) cc_final: 0.8391 (t0) REVERT: R 28 TYR cc_start: 0.8596 (t80) cc_final: 0.8206 (t80) REVERT: S 45 ASP cc_start: 0.8530 (t0) cc_final: 0.8258 (t0) REVERT: T 137 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7799 (mm-30) REVERT: X 24 ASN cc_start: 0.8911 (t0) cc_final: 0.8353 (t0) REVERT: Y 45 ASP cc_start: 0.8682 (t0) cc_final: 0.8445 (t0) REVERT: Y 50 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7521 (mm) REVERT: Y 130 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.8404 (m-80) REVERT: b 127 MET cc_start: 0.9074 (mmm) cc_final: 0.8864 (tpp) REVERT: d 24 ASN cc_start: 0.8430 (t0) cc_final: 0.8055 (t0) REVERT: d 28 TYR cc_start: 0.8879 (t80) cc_final: 0.8492 (t80) REVERT: f 79 GLU cc_start: 0.8549 (tp30) cc_final: 0.8232 (tp30) REVERT: f 145 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8351 (tp) REVERT: f 154 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7888 (mm-30) outliers start: 62 outliers final: 46 residues processed: 594 average time/residue: 0.2407 time to fit residues: 230.3058 Evaluate side-chains 600 residues out of total 4471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 549 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 MET Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain K residue 111 GLU Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain N residue 670 ILE Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 115 MET Chi-restraints excluded: chain R residue 22 ASP Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 144 ASP Chi-restraints excluded: chain T residue 130 PHE Chi-restraints excluded: chain U residue 42 THR Chi-restraints excluded: chain U residue 150 LYS Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain W residue 42 THR Chi-restraints excluded: chain X residue 110 ASP Chi-restraints excluded: chain X residue 111 ASP Chi-restraints excluded: chain X residue 118 ILE Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 84 GLN Chi-restraints excluded: chain Y residue 130 PHE Chi-restraints excluded: chain Y residue 156 ILE Chi-restraints excluded: chain Z residue 25 VAL Chi-restraints excluded: chain Z residue 130 PHE Chi-restraints excluded: chain a residue 42 THR Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 160 ILE Chi-restraints excluded: chain b residue 50 LEU Chi-restraints excluded: chain b residue 71 ASP Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain f residue 112 THR Chi-restraints excluded: chain f residue 130 PHE Chi-restraints excluded: chain f residue 144 ASP Chi-restraints excluded: chain f residue 145 LEU Chi-restraints excluded: chain g residue 160 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 5 optimal weight: 7.9990 chunk 474 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 285 optimal weight: 5.9990 chunk 430 optimal weight: 6.9990 chunk 214 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 362 optimal weight: 7.9990 chunk 188 optimal weight: 0.3980 chunk 286 optimal weight: 10.0000 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 163 GLN N 669 GLN W 24 ASN X 54 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.100163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.079026 restraints weight = 72772.428| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.22 r_work: 0.2854 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 40799 Z= 0.196 Angle : 0.531 8.366 55082 Z= 0.289 Chirality : 0.047 0.165 6386 Planarity : 0.003 0.049 7043 Dihedral : 4.593 56.194 5424 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.32 % Favored : 95.56 % Rotamer: Outliers : 1.45 % Allowed : 12.50 % Favored : 86.04 % 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: -0.06 (0.12), residues: 4978 helix: 2.50 (0.20), residues: 676 sheet: 0.16 (0.13), residues: 1777 loop : -0.88 (0.12), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 218 TYR 0.019 0.001 TYR g 28 PHE 0.024 0.002 PHE g 142 TRP 0.007 0.001 TRP A 91 HIS 0.004 0.001 HIS E 74 Details of bonding type rmsd covalent geometry : bond 0.00481 (40799) covalent geometry : angle 0.53055 (55082) hydrogen bonds : bond 0.04474 ( 1055) hydrogen bonds : angle 4.48136 ( 2775) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 4471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 553 time to evaluate : 1.561 Fit side-chains REVERT: D 59 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8460 (pt0) REVERT: G 95 MET cc_start: 0.9518 (mmm) cc_final: 0.8933 (tpt) REVERT: G 218 ARG cc_start: 0.8980 (mmt90) cc_final: 0.8684 (mtp85) REVERT: L 29 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8006 (tt) REVERT: L 102 GLU cc_start: 0.8602 (pm20) cc_final: 0.8157 (pt0) REVERT: M 671 ASN cc_start: 0.8810 (m110) cc_final: 0.8361 (m110) REVERT: P 50 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8273 (mm) REVERT: R 24 ASN cc_start: 0.8663 (t0) cc_final: 0.8431 (t0) REVERT: R 28 TYR cc_start: 0.8621 (t80) cc_final: 0.8293 (t80) REVERT: S 45 ASP cc_start: 0.8573 (t0) cc_final: 0.8325 (t0) REVERT: S 79 GLU cc_start: 0.9006 (tp30) cc_final: 0.8798 (tp30) REVERT: T 137 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7796 (mm-30) REVERT: X 24 ASN cc_start: 0.8937 (t0) cc_final: 0.8365 (t0) REVERT: X 38 GLN cc_start: 0.7642 (mp10) cc_final: 0.7426 (mp10) REVERT: Y 45 ASP cc_start: 0.8691 (t0) cc_final: 0.8459 (t0) REVERT: Y 50 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7737 (mm) REVERT: Y 130 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8428 (m-80) REVERT: b 127 MET cc_start: 0.9106 (mmm) cc_final: 0.8905 (tpp) REVERT: d 24 ASN cc_start: 0.8442 (t0) cc_final: 0.8081 (t0) REVERT: d 28 TYR cc_start: 0.8851 (t80) cc_final: 0.8499 (t80) REVERT: d 38 GLN cc_start: 0.7373 (mp10) cc_final: 0.6915 (mp10) REVERT: f 79 GLU cc_start: 0.8569 (tp30) cc_final: 0.8263 (tp30) REVERT: f 145 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8364 (tp) REVERT: f 154 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8087 (mm-30) outliers start: 65 outliers final: 53 residues processed: 590 average time/residue: 0.2660 time to fit residues: 251.1401 Evaluate side-chains 603 residues out of total 4471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 545 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain B residue 28 MET Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain J residue 2 TYR Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain K residue 111 GLU Chi-restraints excluded: chain K residue 133 ILE Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain M residue 659 ASP Chi-restraints excluded: chain N residue 670 ILE Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 115 MET Chi-restraints excluded: chain R residue 22 ASP Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 144 ASP Chi-restraints excluded: chain T residue 130 PHE Chi-restraints excluded: chain U residue 42 THR Chi-restraints excluded: chain U residue 150 LYS Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain W residue 42 THR Chi-restraints excluded: chain X residue 110 ASP Chi-restraints excluded: chain X residue 111 ASP Chi-restraints excluded: chain X residue 118 ILE Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 84 GLN Chi-restraints excluded: chain Y residue 115 MET Chi-restraints excluded: chain Y residue 130 PHE Chi-restraints excluded: chain Y residue 150 LYS Chi-restraints excluded: chain Y residue 156 ILE Chi-restraints excluded: chain Z residue 25 VAL Chi-restraints excluded: chain Z residue 130 PHE Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 160 ILE Chi-restraints excluded: chain b residue 50 LEU Chi-restraints excluded: chain b residue 71 ASP Chi-restraints excluded: chain f residue 112 THR Chi-restraints excluded: chain f residue 130 PHE Chi-restraints excluded: chain f residue 144 ASP Chi-restraints excluded: chain f residue 145 LEU Chi-restraints excluded: chain g residue 160 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 302 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 414 optimal weight: 8.9990 chunk 157 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 354 optimal weight: 7.9990 chunk 229 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 163 GLN N 669 GLN W 24 ASN X 54 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.100658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.079530 restraints weight = 72247.252| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.21 r_work: 0.2865 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 40799 Z= 0.170 Angle : 0.518 8.378 55082 Z= 0.283 Chirality : 0.047 0.171 6386 Planarity : 0.003 0.049 7043 Dihedral : 4.563 55.592 5424 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.54 % Favored : 96.34 % Rotamer: Outliers : 1.43 % Allowed : 12.57 % Favored : 86.00 % 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: -0.05 (0.12), residues: 4978 helix: 2.52 (0.20), residues: 676 sheet: 0.17 (0.13), residues: 1765 loop : -0.88 (0.12), residues: 2537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 218 TYR 0.019 0.001 TYR g 28 PHE 0.024 0.001 PHE g 142 TRP 0.008 0.001 TRP D 91 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00415 (40799) covalent geometry : angle 0.51777 (55082) hydrogen bonds : bond 0.04208 ( 1055) hydrogen bonds : angle 4.43024 ( 2775) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 4471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 554 time to evaluate : 1.582 Fit side-chains REVERT: D 59 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8471 (pt0) REVERT: G 95 MET cc_start: 0.9509 (mmm) cc_final: 0.8965 (tpt) REVERT: G 218 ARG cc_start: 0.8986 (mmt90) cc_final: 0.8685 (mtp85) REVERT: L 29 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7977 (tt) REVERT: L 102 GLU cc_start: 0.8622 (pm20) cc_final: 0.8226 (pt0) REVERT: M 671 ASN cc_start: 0.8745 (m110) cc_final: 0.8283 (m110) REVERT: P 50 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8277 (mm) REVERT: R 24 ASN cc_start: 0.8671 (t0) cc_final: 0.8446 (t0) REVERT: R 28 TYR cc_start: 0.8558 (t80) cc_final: 0.8312 (t80) REVERT: S 45 ASP cc_start: 0.8561 (t0) cc_final: 0.8323 (t0) REVERT: S 79 GLU cc_start: 0.8997 (tp30) cc_final: 0.8791 (tp30) REVERT: T 137 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7780 (mm-30) REVERT: X 24 ASN cc_start: 0.8926 (t0) cc_final: 0.8357 (t0) REVERT: X 38 GLN cc_start: 0.7611 (mp10) cc_final: 0.7377 (mp10) REVERT: Y 45 ASP cc_start: 0.8646 (t0) cc_final: 0.8424 (t0) REVERT: Y 50 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7704 (mm) REVERT: Y 116 ARG cc_start: 0.8719 (ptt90) cc_final: 0.8454 (ptt90) REVERT: Y 130 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.8496 (m-80) REVERT: a 31 ASP cc_start: 0.6118 (OUTLIER) cc_final: 0.5704 (t70) REVERT: d 24 ASN cc_start: 0.8444 (t0) cc_final: 0.8095 (t0) REVERT: d 28 TYR cc_start: 0.8863 (t80) cc_final: 0.8491 (t80) REVERT: d 38 GLN cc_start: 0.7364 (mp10) cc_final: 0.6907 (mp10) REVERT: f 79 GLU cc_start: 0.8567 (tp30) cc_final: 0.8266 (tp30) REVERT: f 145 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8366 (tp) REVERT: f 154 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8040 (mm-30) outliers start: 64 outliers final: 55 residues processed: 593 average time/residue: 0.2604 time to fit residues: 247.8479 Evaluate side-chains 613 residues out of total 4471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 552 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain B residue 28 MET Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain J residue 2 TYR Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain K residue 111 GLU Chi-restraints excluded: chain K residue 133 ILE Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain M residue 659 ASP Chi-restraints excluded: chain N residue 670 ILE Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 115 MET Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain R residue 22 ASP Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 144 ASP Chi-restraints excluded: chain T residue 130 PHE Chi-restraints excluded: chain U residue 42 THR Chi-restraints excluded: chain U residue 150 LYS Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain U residue 156 ILE Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 147 THR Chi-restraints excluded: chain W residue 42 THR Chi-restraints excluded: chain X residue 111 ASP Chi-restraints excluded: chain X residue 118 ILE Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 84 GLN Chi-restraints excluded: chain Y residue 115 MET Chi-restraints excluded: chain Y residue 130 PHE Chi-restraints excluded: chain Y residue 150 LYS Chi-restraints excluded: chain Z residue 25 VAL Chi-restraints excluded: chain Z residue 130 PHE Chi-restraints excluded: chain a residue 31 ASP Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 160 ILE Chi-restraints excluded: chain b residue 50 LEU Chi-restraints excluded: chain b residue 71 ASP Chi-restraints excluded: chain f residue 112 THR Chi-restraints excluded: chain f residue 144 ASP Chi-restraints excluded: chain f residue 145 LEU Chi-restraints excluded: chain g residue 50 LEU Chi-restraints excluded: chain g residue 160 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 96 optimal weight: 3.9990 chunk 292 optimal weight: 2.9990 chunk 330 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 111 optimal weight: 0.0870 chunk 299 optimal weight: 10.0000 chunk 434 optimal weight: 8.9990 chunk 143 optimal weight: 0.5980 chunk 259 optimal weight: 0.9980 chunk 436 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 163 GLN N 669 GLN W 24 ASN X 54 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.104331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.083183 restraints weight = 71613.239| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.21 r_work: 0.2928 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 40799 Z= 0.086 Angle : 0.463 8.071 55082 Z= 0.252 Chirality : 0.045 0.172 6386 Planarity : 0.002 0.049 7043 Dihedral : 4.037 23.728 5422 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.75 % Favored : 97.15 % Rotamer: Outliers : 1.19 % Allowed : 12.99 % Favored : 85.82 % 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: 0.24 (0.12), residues: 4978 helix: 2.73 (0.21), residues: 679 sheet: 0.40 (0.13), residues: 1777 loop : -0.73 (0.12), residues: 2522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 218 TYR 0.016 0.001 TYR g 28 PHE 0.024 0.001 PHE g 142 TRP 0.008 0.001 TRP D 91 HIS 0.002 0.000 HIS b 63 Details of bonding type rmsd covalent geometry : bond 0.00192 (40799) covalent geometry : angle 0.46348 (55082) hydrogen bonds : bond 0.02806 ( 1055) hydrogen bonds : angle 4.04282 ( 2775) =============================================================================== Job complete usr+sys time: 12003.41 seconds wall clock time: 205 minutes 8.01 seconds (12308.01 seconds total)