Starting phenix.real_space_refine on Sat Sep 12 13:38:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cha_30373/09_2026/7cha_30373.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cha_30373/09_2026/7cha_30373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7cha_30373/09_2026/7cha_30373.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cha_30373/09_2026/7cha_30373.cif" model { file = "/net/cci-nas-00/data/ceres_data/7cha_30373/09_2026/7cha_30373.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cha_30373/09_2026/7cha_30373.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cha_30373/09_2026/7cha_30373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cha_30373/09_2026/7cha_30373.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 13 5.49 5 S 44 5.16 5 C 10414 2.51 5 N 2701 2.21 5 O 3059 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 120 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16231 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1085 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 1, 'TRANS': 145} Chain: "B" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1076 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 1, 'TRANS': 144} Chain: "C" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1076 Classifications: {'peptide': 146} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 143} Chain: "D" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1082 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 1, 'TRANS': 145} Chain: "E" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1098 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 1, 'TRANS': 147} Chain: "F" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1068 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 1, 'TRANS': 143} Chain: "G" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1939 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 7, 'TRANS': 250} Chain: "H" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1939 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 7, 'TRANS': 250} Chain: "I" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2028 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 16, 'TRANS': 245} Chain: "K" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 721 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "G" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 176 Unusual residues: {'LPP': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 132 Unusual residues: {'LPP': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: J, L Time building chain proxies: 4.51, per 1000 atoms: 0.28 Number of scatterers: 16231 At special positions: 0 Unit cell: (98.8, 122.72, 145.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 13 15.00 O 3059 8.00 N 2701 7.00 C 10414 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=13, symmetry=0 Number of additional bonds: simple=13, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 803.0 milliseconds 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3764 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 19 sheets defined 45.8% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 2 through 21 Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 31 through 36 Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.786A pdb=" N PHE B 145 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 27 removed outlier: 4.278A pdb=" N ILE C 8 " --> pdb=" O ARG C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.506A pdb=" N PHE C 145 " --> pdb=" O LEU C 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 26 Processing helix chain 'D' and resid 137 through 144 Processing helix chain 'E' and resid 3 through 20 Processing helix chain 'E' and resid 139 through 147 Processing helix chain 'F' and resid 4 through 7 Processing helix chain 'F' and resid 8 through 26 removed outlier: 3.741A pdb=" N ALA F 20 " --> pdb=" O ALA F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 Processing helix chain 'G' and resid 6 through 37 Processing helix chain 'G' and resid 45 through 56 Processing helix chain 'G' and resid 59 through 84 removed outlier: 4.013A pdb=" N ILE G 63 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN G 80 " --> pdb=" O LEU G 76 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER G 84 " --> pdb=" O ASN G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 86 No H-bonds generated for 'chain 'G' and resid 85 through 86' Processing helix chain 'G' and resid 87 through 90 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'G' and resid 97 through 102 removed outlier: 3.618A pdb=" N GLU G 102 " --> pdb=" O THR G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 113 Processing helix chain 'G' and resid 120 through 130 Processing helix chain 'G' and resid 131 through 140 removed outlier: 3.716A pdb=" N LEU G 136 " --> pdb=" O GLN G 132 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU G 137 " --> pdb=" O LEU G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 147 Processing helix chain 'G' and resid 148 through 157 Processing helix chain 'G' and resid 158 through 181 Processing helix chain 'G' and resid 185 through 195 removed outlier: 3.555A pdb=" N PHE G 189 " --> pdb=" O TYR G 185 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TRP G 190 " --> pdb=" O GLU G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 197 No H-bonds generated for 'chain 'G' and resid 196 through 197' Processing helix chain 'G' and resid 198 through 201 Processing helix chain 'G' and resid 202 through 228 removed outlier: 3.538A pdb=" N PHE G 213 " --> pdb=" O LYS G 209 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL G 222 " --> pdb=" O THR G 218 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLY G 225 " --> pdb=" O ALA G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 260 removed outlier: 3.602A pdb=" N SER G 236 " --> pdb=" O SER G 232 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR G 240 " --> pdb=" O SER G 236 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL G 243 " --> pdb=" O THR G 239 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA G 246 " --> pdb=" O THR G 242 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL G 250 " --> pdb=" O ALA G 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 37 Processing helix chain 'H' and resid 45 through 56 Processing helix chain 'H' and resid 59 through 84 removed outlier: 4.014A pdb=" N ILE H 63 " --> pdb=" O SER H 59 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN H 80 " --> pdb=" O LEU H 76 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER H 84 " --> pdb=" O ASN H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 86 No H-bonds generated for 'chain 'H' and resid 85 through 86' Processing helix chain 'H' and resid 87 through 90 Processing helix chain 'H' and resid 91 through 96 Processing helix chain 'H' and resid 97 through 102 removed outlier: 3.619A pdb=" N GLU H 102 " --> pdb=" O THR H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 113 Processing helix chain 'H' and resid 120 through 130 Processing helix chain 'H' and resid 131 through 140 removed outlier: 3.716A pdb=" N LEU H 136 " --> pdb=" O GLN H 132 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU H 137 " --> pdb=" O LEU H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 147 Processing helix chain 'H' and resid 148 through 157 Processing helix chain 'H' and resid 158 through 181 Processing helix chain 'H' and resid 185 through 195 removed outlier: 3.556A pdb=" N PHE H 189 " --> pdb=" O TYR H 185 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TRP H 190 " --> pdb=" O GLU H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 197 No H-bonds generated for 'chain 'H' and resid 196 through 197' Processing helix chain 'H' and resid 198 through 201 Processing helix chain 'H' and resid 202 through 228 removed outlier: 3.537A pdb=" N PHE H 213 " --> pdb=" O LYS H 209 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL H 222 " --> pdb=" O THR H 218 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLY H 225 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 231 through 260 removed outlier: 3.602A pdb=" N SER H 236 " --> pdb=" O SER H 232 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR H 240 " --> pdb=" O SER H 236 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL H 243 " --> pdb=" O THR H 239 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA H 246 " --> pdb=" O THR H 242 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL H 250 " --> pdb=" O ALA H 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 55 Processing helix chain 'I' and resid 76 through 84 removed outlier: 3.926A pdb=" N ASP I 82 " --> pdb=" O GLY I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 114 Proline residue: I 109 - end of helix Processing helix chain 'I' and resid 117 through 133 removed outlier: 3.581A pdb=" N ARG I 122 " --> pdb=" O GLU I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 145 Processing helix chain 'I' and resid 148 through 160 removed outlier: 3.851A pdb=" N ARG I 152 " --> pdb=" O GLY I 148 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA I 154 " --> pdb=" O LYS I 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 193 removed outlier: 3.585A pdb=" N ARG I 188 " --> pdb=" O VAL I 184 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN I 191 " --> pdb=" O ILE I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 212 removed outlier: 3.767A pdb=" N THR I 208 " --> pdb=" O ASP I 204 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 234 removed outlier: 3.702A pdb=" N GLU I 234 " --> pdb=" O ASP I 230 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 244 Processing helix chain 'I' and resid 262 through 267 Processing helix chain 'J' and resid 46 through 55 Processing helix chain 'J' and resid 76 through 84 removed outlier: 3.926A pdb=" N ASP J 82 " --> pdb=" O GLY J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 114 Proline residue: J 109 - end of helix Processing helix chain 'J' and resid 117 through 133 removed outlier: 3.581A pdb=" N ARG J 122 " --> pdb=" O GLU J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 145 Processing helix chain 'J' and resid 148 through 160 removed outlier: 3.851A pdb=" N ARG J 152 " --> pdb=" O GLY J 148 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA J 154 " --> pdb=" O LYS J 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 193 removed outlier: 3.586A pdb=" N ARG J 188 " --> pdb=" O VAL J 184 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN J 191 " --> pdb=" O ILE J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 204 through 212 removed outlier: 3.768A pdb=" N THR J 208 " --> pdb=" O ASP J 204 " (cutoff:3.500A) Processing helix chain 'J' and resid 228 through 234 removed outlier: 3.703A pdb=" N GLU J 234 " --> pdb=" O ASP J 230 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 244 Processing helix chain 'J' and resid 262 through 267 Processing helix chain 'K' and resid 24 through 34 removed outlier: 3.648A pdb=" N LEU K 28 " --> pdb=" O SER K 24 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG K 34 " --> pdb=" O GLU K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 72 removed outlier: 3.539A pdb=" N ILE K 59 " --> pdb=" O SER K 55 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE K 66 " --> pdb=" O LEU K 62 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP K 68 " --> pdb=" O ALA K 64 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA K 69 " --> pdb=" O PHE K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 92 removed outlier: 3.792A pdb=" N SER K 92 " --> pdb=" O ILE K 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 34 removed outlier: 3.648A pdb=" N LEU L 28 " --> pdb=" O SER L 24 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG L 34 " --> pdb=" O GLU L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 72 removed outlier: 3.540A pdb=" N ILE L 59 " --> pdb=" O SER L 55 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE L 66 " --> pdb=" O LEU L 62 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP L 68 " --> pdb=" O ALA L 64 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA L 69 " --> pdb=" O PHE L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 92 removed outlier: 3.792A pdb=" N SER L 92 " --> pdb=" O ILE L 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 46 removed outlier: 5.991A pdb=" N GLU A 85 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N VAL A 68 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 66 removed outlier: 6.566A pdb=" N VAL A 58 " --> pdb=" O ILE A 65 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ALA A 99 " --> pdb=" O GLN A 133 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 39 through 46 removed outlier: 5.826A pdb=" N GLU B 85 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N VAL B 68 " --> pdb=" O GLU B 85 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ASN B 87 " --> pdb=" O GLY B 66 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N GLY B 66 " --> pdb=" O ASN B 87 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N THR B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LEU B 60 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LYS B 57 " --> pdb=" O ILE B 112 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N ILE B 114 " --> pdb=" O LYS B 57 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR B 59 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 133 " --> pdb=" O ALA B 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 40 through 46 removed outlier: 3.644A pdb=" N TYR C 40 " --> pdb=" O ILE C 86 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ARG C 81 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL C 71 " --> pdb=" O ARG C 81 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR C 83 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU C 85 " --> pdb=" O LYS C 67 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LYS C 67 " --> pdb=" O GLU C 85 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL C 58 " --> pdb=" O ILE C 65 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LYS C 57 " --> pdb=" O ILE C 112 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ILE C 114 " --> pdb=" O LYS C 57 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR C 59 " --> pdb=" O ILE C 114 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 39 through 46 removed outlier: 5.776A pdb=" N GLU D 85 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N VAL D 68 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ASN D 87 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLY D 66 " --> pdb=" O ASN D 87 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL D 58 " --> pdb=" O ILE D 65 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LYS D 57 " --> pdb=" O ILE D 112 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE D 114 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR D 59 " --> pdb=" O ILE D 114 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 39 through 46 removed outlier: 3.924A pdb=" N THR E 79 " --> pdb=" O ASP E 74 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLU E 85 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N VAL E 68 " --> pdb=" O GLU E 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 63 through 66 removed outlier: 6.523A pdb=" N VAL E 58 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA E 99 " --> pdb=" O GLN E 133 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 40 through 46 removed outlier: 6.010A pdb=" N GLU F 85 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N VAL F 68 " --> pdb=" O GLU F 85 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 63 through 66 removed outlier: 6.778A pdb=" N VAL F 58 " --> pdb=" O ILE F 65 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 24 through 32 removed outlier: 5.855A pdb=" N ASP I 25 " --> pdb=" O THR I 15 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N THR I 15 " --> pdb=" O ASP I 25 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ILE I 27 " --> pdb=" O GLY I 13 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL I 29 " --> pdb=" O LEU I 11 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU I 14 " --> pdb=" O LYS I 62 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LYS I 62 " --> pdb=" O LEU I 14 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 37 through 39 removed outlier: 6.704A pdb=" N GLY I 88 " --> pdb=" O LEU I 167 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N ASP I 169 " --> pdb=" O GLY I 88 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU I 90 " --> pdb=" O ASP I 169 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 215 through 219 removed outlier: 7.005A pdb=" N ILE I 215 " --> pdb=" O HIS I 226 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N HIS I 226 " --> pdb=" O ILE I 215 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ILE I 217 " --> pdb=" O LEU I 224 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 24 through 32 removed outlier: 5.855A pdb=" N ASP J 25 " --> pdb=" O THR J 15 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N THR J 15 " --> pdb=" O ASP J 25 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ILE J 27 " --> pdb=" O GLY J 13 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL J 29 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU J 14 " --> pdb=" O LYS J 62 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LYS J 62 " --> pdb=" O LEU J 14 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 37 through 39 removed outlier: 6.705A pdb=" N GLY J 88 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ASP J 169 " --> pdb=" O GLY J 88 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU J 90 " --> pdb=" O ASP J 169 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 215 through 219 removed outlier: 7.005A pdb=" N ILE J 215 " --> pdb=" O HIS J 226 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N HIS J 226 " --> pdb=" O ILE J 215 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ILE J 217 " --> pdb=" O LEU J 224 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 6 through 7 removed outlier: 3.631A pdb=" N ARG K 7 " --> pdb=" O GLN K 15 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU K 16 " --> pdb=" O ASP K 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 19 through 20 Processing sheet with id=AB9, first strand: chain 'L' and resid 6 through 7 removed outlier: 3.631A pdb=" N ARG L 7 " --> pdb=" O GLN L 15 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU L 16 " --> pdb=" O ASP L 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 19 through 20 777 hydrogen bonds defined for protein. 2235 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: 2.59 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2683 1.30 - 1.43: 3792 1.43 - 1.55: 9858 1.55 - 1.68: 25 1.68 - 1.81: 84 Bond restraints: 16442 Sorted by residual: bond pdb=" O5 LPP H 301 " pdb=" P1 LPP H 301 " ideal model delta sigma weight residual 2.278 1.638 0.640 2.00e-02 2.50e+03 1.02e+03 bond pdb=" O5 LPP G 302 " pdb=" P1 LPP G 302 " ideal model delta sigma weight residual 2.278 1.643 0.635 2.00e-02 2.50e+03 1.01e+03 bond pdb=" O5 LPP H 303 " pdb=" P1 LPP H 303 " ideal model delta sigma weight residual 2.278 1.646 0.632 2.00e-02 2.50e+03 9.97e+02 bond pdb=" O5 LPP G 304 " pdb=" P1 LPP G 304 " ideal model delta sigma weight residual 2.278 1.647 0.631 2.00e-02 2.50e+03 9.96e+02 bond pdb=" O5 LPP H 302 " pdb=" P1 LPP H 302 " ideal model delta sigma weight residual 2.278 1.647 0.631 2.00e-02 2.50e+03 9.95e+02 ... (remaining 16437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.70: 22185 9.70 - 19.39: 40 19.39 - 29.09: 7 29.09 - 38.78: 14 38.78 - 48.48: 7 Bond angle restraints: 22253 Sorted by residual: angle pdb=" O4 LPP H 301 " pdb=" P1 LPP H 301 " pdb=" O5 LPP H 301 " ideal model delta sigma weight residual 62.99 111.47 -48.48 3.00e+00 1.11e-01 2.61e+02 angle pdb=" O4 LPP G 301 " pdb=" P1 LPP G 301 " pdb=" O5 LPP G 301 " ideal model delta sigma weight residual 62.99 110.16 -47.17 3.00e+00 1.11e-01 2.47e+02 angle pdb=" O4 LPP G 303 " pdb=" P1 LPP G 303 " pdb=" O5 LPP G 303 " ideal model delta sigma weight residual 62.99 110.05 -47.06 3.00e+00 1.11e-01 2.46e+02 angle pdb=" O4 LPP G 304 " pdb=" P1 LPP G 304 " pdb=" O5 LPP G 304 " ideal model delta sigma weight residual 62.99 109.76 -46.77 3.00e+00 1.11e-01 2.43e+02 angle pdb=" O4 LPP H 303 " pdb=" P1 LPP H 303 " pdb=" O5 LPP H 303 " ideal model delta sigma weight residual 62.99 109.27 -46.28 3.00e+00 1.11e-01 2.38e+02 ... (remaining 22248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.33: 8726 19.33 - 38.66: 825 38.66 - 57.99: 285 57.99 - 77.32: 41 77.32 - 96.65: 5 Dihedral angle restraints: 9882 sinusoidal: 3954 harmonic: 5928 Sorted by residual: dihedral pdb=" CA SER L 92 " pdb=" C SER L 92 " pdb=" N SER L 93 " pdb=" CA SER L 93 " ideal model delta harmonic sigma weight residual -180.00 -147.53 -32.47 0 5.00e+00 4.00e-02 4.22e+01 dihedral pdb=" CA SER K 92 " pdb=" C SER K 92 " pdb=" N SER K 93 " pdb=" CA SER K 93 " ideal model delta harmonic sigma weight residual -180.00 -147.53 -32.47 0 5.00e+00 4.00e-02 4.22e+01 dihedral pdb=" CA SER F 32 " pdb=" C SER F 32 " pdb=" N VAL F 33 " pdb=" CA VAL F 33 " ideal model delta harmonic sigma weight residual -180.00 -147.98 -32.02 0 5.00e+00 4.00e-02 4.10e+01 ... (remaining 9879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2261 0.065 - 0.130: 389 0.130 - 0.195: 33 0.195 - 0.261: 6 0.261 - 0.326: 3 Chirality restraints: 2692 Sorted by residual: chirality pdb=" C7 LPP H 301 " pdb=" C6 LPP H 301 " pdb=" C8 LPP H 301 " pdb=" O9 LPP H 301 " both_signs ideal model delta sigma weight residual False -2.69 -2.37 -0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" C3' ANP I 301 " pdb=" C2' ANP I 301 " pdb=" C4' ANP I 301 " pdb=" O3' ANP I 301 " both_signs ideal model delta sigma weight residual False -2.36 -2.68 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C3' ANP J 301 " pdb=" C2' ANP J 301 " pdb=" C4' ANP J 301 " pdb=" O3' ANP J 301 " both_signs ideal model delta sigma weight residual False -2.36 -2.68 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 2689 not shown) Planarity restraints: 2779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR J 256 " -0.039 5.00e-02 4.00e+02 5.87e-02 5.52e+00 pdb=" N PRO J 257 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO J 257 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO J 257 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR I 256 " -0.039 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO I 257 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO I 257 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO I 257 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA I 193 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.06e+00 pdb=" C ALA I 193 " -0.035 2.00e-02 2.50e+03 pdb=" O ALA I 193 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU I 194 " 0.012 2.00e-02 2.50e+03 ... (remaining 2776 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 356 2.61 - 3.18: 16428 3.18 - 3.75: 25257 3.75 - 4.33: 34810 4.33 - 4.90: 55236 Nonbonded interactions: 132087 Sorted by model distance: nonbonded pdb=" O ALA B 25 " pdb=" OG SER B 29 " model vdw 2.033 3.040 nonbonded pdb=" O ALA C 99 " pdb=" OG1 THR C 132 " model vdw 2.111 3.040 nonbonded pdb=" CD2 TYR H 85 " pdb=" O10 LPP G 304 " model vdw 2.113 2.672 nonbonded pdb=" OD2 ASP J 123 " pdb=" NH2 ARG L 67 " model vdw 2.115 3.120 nonbonded pdb=" OD2 ASP D 74 " pdb=" OG SER D 77 " model vdw 2.123 3.040 ... (remaining 132082 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 147) selection = (chain 'B' and resid 3 through 147) selection = (chain 'C' and resid 3 through 147) selection = (chain 'D' and resid 3 through 147) selection = (chain 'E' and resid 3 through 147) selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 5 through 303) selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.230 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 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 : 0.017 0.640 16455 Z= 0.838 Angle : 1.685 48.481 22253 Z= 0.692 Chirality : 0.050 0.326 2692 Planarity : 0.005 0.059 2779 Dihedral : 17.308 96.650 6118 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 24.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 14.44 % Favored : 85.52 % Rotamer: Outliers : 5.12 % Allowed : 11.54 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -4.83 (0.14), residues: 2092 helix: -2.74 (0.14), residues: 863 sheet: -2.59 (0.26), residues: 297 loop : -3.86 (0.15), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 37 TYR 0.019 0.002 TYR F 40 PHE 0.017 0.002 PHE F 145 TRP 0.011 0.002 TRP H 153 HIS 0.003 0.001 HIS I 203 Details of bonding type rmsd/Z covalent geometry : bond 0.01707 / 0.84 (16442) covalent geometry : angle 1.68494 / 0.69 (22253) hydrogen bonds : bond 0.15686 / 10.28 ( 777) hydrogen bonds : angle 7.70270 / 5.36 ( 2235) Misc. bond : bond 0.00355 / 0.20 ( 13) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 528 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8751 (t0) cc_final: 0.8507 (t0) REVERT: B 19 LEU cc_start: 0.8782 (mt) cc_final: 0.8507 (tt) REVERT: B 133 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7912 (mm110) REVERT: C 18 LEU cc_start: 0.9051 (mp) cc_final: 0.8829 (mp) REVERT: C 90 VAL cc_start: 0.7317 (t) cc_final: 0.7041 (t) REVERT: D 84 MET cc_start: 0.8225 (pmm) cc_final: 0.7952 (pmm) REVERT: E 7 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7595 (mt-10) REVERT: E 14 LEU cc_start: 0.8712 (tp) cc_final: 0.8369 (tt) REVERT: E 111 TYR cc_start: 0.8999 (p90) cc_final: 0.8402 (p90) REVERT: F 67 LYS cc_start: 0.8893 (ptmt) cc_final: 0.8495 (ptpt) REVERT: F 101 ILE cc_start: 0.9506 (mp) cc_final: 0.9277 (mt) REVERT: G 7 LEU cc_start: 0.7568 (pp) cc_final: 0.7320 (mt) REVERT: G 8 GLU cc_start: 0.8249 (tt0) cc_final: 0.7885 (mp0) REVERT: G 93 GLN cc_start: 0.8519 (pt0) cc_final: 0.8317 (mt0) REVERT: G 167 SER cc_start: 0.9358 (OUTLIER) cc_final: 0.9149 (m) REVERT: G 172 TRP cc_start: 0.7370 (t60) cc_final: 0.6304 (m-10) REVERT: G 186 GLU cc_start: 0.8211 (mp0) cc_final: 0.8008 (mp0) REVERT: H 19 ASP cc_start: 0.8765 (OUTLIER) cc_final: 0.8419 (m-30) REVERT: H 185 TYR cc_start: 0.8100 (t80) cc_final: 0.7372 (t80) REVERT: H 223 TYR cc_start: 0.9148 (t80) cc_final: 0.8781 (t80) REVERT: I 10 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7111 (mp0) REVERT: I 101 ASP cc_start: 0.8212 (p0) cc_final: 0.7958 (p0) REVERT: I 159 ILE cc_start: 0.9552 (pt) cc_final: 0.9299 (mt) REVERT: I 175 GLN cc_start: 0.8515 (pm20) cc_final: 0.8279 (pm20) REVERT: I 202 SER cc_start: 0.8815 (t) cc_final: 0.8604 (t) REVERT: J 233 LYS cc_start: 0.8889 (tppp) cc_final: 0.8627 (mmmm) REVERT: K 45 VAL cc_start: 0.8134 (t) cc_final: 0.7888 (p) REVERT: K 70 ARG cc_start: 0.8400 (ttt-90) cc_final: 0.8075 (ttp80) REVERT: L 44 LEU cc_start: 0.6448 (OUTLIER) cc_final: 0.5983 (mm) outliers start: 87 outliers final: 18 residues processed: 563 average time/residue: 0.1383 time to fit residues: 112.1919 Evaluate side-chains 383 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 362 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain K residue 37 ARG Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 61 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN A 88 GLN D 92 ASN E 2 GLN E 35 ASN E 87 ASN ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN F 133 GLN ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN G 195 ASN G 224 GLN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 26 ASN I 86 GLN ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 68 ASN J 86 GLN J 105 ASN ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 191 ASN ** J 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.111572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.083781 restraints weight = 40592.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.083001 restraints weight = 33467.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.083782 restraints weight = 27734.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.084144 restraints weight = 22255.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.084255 restraints weight = 20239.889| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16455 Z= 0.174 Angle : 0.800 13.415 22253 Z= 0.402 Chirality : 0.046 0.234 2692 Planarity : 0.006 0.111 2779 Dihedral : 13.885 90.258 2637 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 4.95 % Allowed : 21.02 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.34 (0.16), residues: 2092 helix: -1.16 (0.16), residues: 879 sheet: -2.32 (0.27), residues: 297 loop : -3.24 (0.16), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 75 TYR 0.024 0.002 TYR G 79 PHE 0.024 0.002 PHE G 213 TRP 0.024 0.002 TRP I 66 HIS 0.003 0.001 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (16442) covalent geometry : angle 0.79969 / 0.40 (22253) hydrogen bonds : bond 0.04622 / 3.18 ( 777) hydrogen bonds : angle 5.60131 / 3.89 ( 2235) Misc. bond : bond 0.00300 / 0.20 ( 13) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 463 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8839 (t0) cc_final: 0.8543 (t0) REVERT: B 19 LEU cc_start: 0.8755 (mt) cc_final: 0.8480 (tt) REVERT: C 3 THR cc_start: 0.5957 (OUTLIER) cc_final: 0.5438 (t) REVERT: C 65 ILE cc_start: 0.6888 (OUTLIER) cc_final: 0.6549 (tp) REVERT: C 67 LYS cc_start: 0.9172 (ptpt) cc_final: 0.8769 (ptpt) REVERT: C 69 THR cc_start: 0.8252 (p) cc_final: 0.7828 (t) REVERT: D 67 LYS cc_start: 0.8891 (ptpt) cc_final: 0.7911 (mmtm) REVERT: E 48 ASN cc_start: 0.8083 (t0) cc_final: 0.7478 (m-40) REVERT: F 4 ARG cc_start: 0.7513 (mtt180) cc_final: 0.6765 (ttm110) REVERT: F 67 LYS cc_start: 0.8883 (ptmt) cc_final: 0.8532 (ttpp) REVERT: G 93 GLN cc_start: 0.8541 (pt0) cc_final: 0.8340 (tt0) REVERT: G 132 GLN cc_start: 0.8942 (tt0) cc_final: 0.8701 (tt0) REVERT: G 172 TRP cc_start: 0.7171 (t60) cc_final: 0.6240 (m-10) REVERT: G 185 TYR cc_start: 0.6733 (t80) cc_final: 0.6529 (t80) REVERT: G 254 ASP cc_start: 0.8813 (t0) cc_final: 0.8588 (t0) REVERT: G 255 PHE cc_start: 0.8671 (t80) cc_final: 0.8443 (t80) REVERT: H 223 TYR cc_start: 0.8984 (t80) cc_final: 0.8623 (t80) REVERT: I 10 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7181 (mp0) REVERT: I 116 LEU cc_start: 0.9022 (mt) cc_final: 0.8556 (mp) REVERT: I 139 GLU cc_start: 0.7780 (tp30) cc_final: 0.7566 (tp30) REVERT: I 159 ILE cc_start: 0.9601 (pt) cc_final: 0.9399 (mt) REVERT: J 105 ASN cc_start: 0.9031 (OUTLIER) cc_final: 0.8708 (t0) REVERT: K 70 ARG cc_start: 0.8487 (ttt-90) cc_final: 0.8202 (ttp80) REVERT: L 87 GLU cc_start: 0.8808 (tt0) cc_final: 0.8513 (tt0) outliers start: 84 outliers final: 44 residues processed: 508 average time/residue: 0.1336 time to fit residues: 100.3855 Evaluate side-chains 399 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 352 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 232 LEU Chi-restraints excluded: chain I residue 235 THR Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain J residue 105 ASN Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 91 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 70 optimal weight: 6.9990 chunk 202 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 3 optimal weight: 20.0000 chunk 118 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 89 optimal weight: 0.2980 chunk 163 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 91 ASN F 133 GLN G 77 GLN ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 ASN H 205 ASN I 68 ASN I 86 GLN ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 ASN J 105 ASN ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.113620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.086655 restraints weight = 42299.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.086150 restraints weight = 37376.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.086638 restraints weight = 28329.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.087043 restraints weight = 24988.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.087118 restraints weight = 24000.001| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16455 Z= 0.175 Angle : 0.775 10.021 22253 Z= 0.390 Chirality : 0.046 0.296 2692 Planarity : 0.005 0.054 2779 Dihedral : 13.040 92.382 2611 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 6.36 % Allowed : 22.91 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.17), residues: 2092 helix: -0.63 (0.17), residues: 877 sheet: -1.98 (0.28), residues: 293 loop : -2.94 (0.18), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 7 TYR 0.036 0.002 TYR G 85 PHE 0.033 0.002 PHE G 156 TRP 0.010 0.002 TRP J 66 HIS 0.003 0.001 HIS J 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (16442) covalent geometry : angle 0.77504 / 0.39 (22253) hydrogen bonds : bond 0.04224 / 2.94 ( 777) hydrogen bonds : angle 5.45058 / 3.77 ( 2235) Misc. bond : bond 0.00302 / 0.20 ( 13) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 393 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8794 (t0) cc_final: 0.8484 (t0) REVERT: B 19 LEU cc_start: 0.8790 (mt) cc_final: 0.8470 (tt) REVERT: C 18 LEU cc_start: 0.9123 (mt) cc_final: 0.8851 (mp) REVERT: D 84 MET cc_start: 0.8162 (pmm) cc_final: 0.7721 (pmm) REVERT: D 86 ILE cc_start: 0.7800 (mp) cc_final: 0.7580 (pt) REVERT: E 7 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7496 (mt-10) REVERT: E 48 ASN cc_start: 0.7923 (t0) cc_final: 0.7273 (m-40) REVERT: E 101 ILE cc_start: 0.9328 (mp) cc_final: 0.9106 (mt) REVERT: F 4 ARG cc_start: 0.7580 (mtt180) cc_final: 0.6702 (ttm110) REVERT: F 47 ASP cc_start: 0.8150 (m-30) cc_final: 0.7779 (t0) REVERT: F 67 LYS cc_start: 0.8719 (ptmt) cc_final: 0.8429 (ttpp) REVERT: G 172 TRP cc_start: 0.7292 (t60) cc_final: 0.6342 (m-10) REVERT: G 255 PHE cc_start: 0.8495 (t80) cc_final: 0.8181 (t80) REVERT: H 176 MET cc_start: 0.7144 (tpt) cc_final: 0.6840 (tmm) REVERT: H 201 GLU cc_start: 0.8039 (mp0) cc_final: 0.7768 (mp0) REVERT: H 223 TYR cc_start: 0.8860 (t80) cc_final: 0.8614 (t80) REVERT: I 159 ILE cc_start: 0.9582 (pt) cc_final: 0.9321 (mt) REVERT: J 51 LEU cc_start: 0.9437 (tp) cc_final: 0.9179 (tp) REVERT: J 105 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8733 (t0) REVERT: J 144 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7836 (tm-30) REVERT: K 8 GLU cc_start: 0.7799 (tp30) cc_final: 0.6943 (tp30) REVERT: K 70 ARG cc_start: 0.8416 (ttt-90) cc_final: 0.8144 (ttp80) REVERT: L 31 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7053 (pp30) REVERT: L 87 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8381 (tt0) outliers start: 108 outliers final: 62 residues processed: 458 average time/residue: 0.1260 time to fit residues: 86.9825 Evaluate side-chains 403 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 338 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 202 SER Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain J residue 105 ASN Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain J residue 150 LYS Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain L residue 31 GLN Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 87 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 203 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 193 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 45 optimal weight: 30.0000 chunk 30 optimal weight: 0.5980 chunk 104 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 ASN ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 GLN ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 ASN ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 ASN ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.111858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.081547 restraints weight = 40722.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.082106 restraints weight = 27292.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.082843 restraints weight = 19980.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.083002 restraints weight = 16630.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.083143 restraints weight = 15638.038| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16455 Z= 0.168 Angle : 0.758 11.551 22253 Z= 0.381 Chirality : 0.045 0.290 2692 Planarity : 0.004 0.052 2779 Dihedral : 12.449 95.314 2607 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 6.65 % Allowed : 24.09 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.17), residues: 2092 helix: -0.37 (0.17), residues: 878 sheet: -1.77 (0.29), residues: 292 loop : -2.84 (0.18), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 86 TYR 0.042 0.002 TYR D 40 PHE 0.026 0.002 PHE G 213 TRP 0.008 0.001 TRP J 66 HIS 0.003 0.001 HIS J 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (16442) covalent geometry : angle 0.75806 / 0.38 (22253) hydrogen bonds : bond 0.04082 / 2.84 ( 777) hydrogen bonds : angle 5.35421 / 3.71 ( 2235) Misc. bond : bond 0.00378 / 0.22 ( 13) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 382 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 THR cc_start: 0.6749 (t) cc_final: 0.6515 (t) REVERT: A 42 VAL cc_start: 0.6823 (OUTLIER) cc_final: 0.6472 (p) REVERT: A 48 ASN cc_start: 0.9052 (t0) cc_final: 0.8746 (t0) REVERT: A 111 TYR cc_start: 0.8798 (p90) cc_final: 0.8505 (p90) REVERT: B 19 LEU cc_start: 0.8680 (mt) cc_final: 0.8394 (tt) REVERT: B 40 TYR cc_start: 0.7635 (m-10) cc_final: 0.7422 (m-10) REVERT: B 120 GLU cc_start: 0.7346 (tm-30) cc_final: 0.7126 (tm-30) REVERT: D 75 ARG cc_start: 0.6338 (mtp-110) cc_final: 0.6073 (mmm160) REVERT: E 48 ASN cc_start: 0.8293 (t0) cc_final: 0.7497 (m-40) REVERT: F 4 ARG cc_start: 0.7887 (mtt180) cc_final: 0.6790 (ttm110) REVERT: F 47 ASP cc_start: 0.8327 (m-30) cc_final: 0.7796 (t0) REVERT: F 67 LYS cc_start: 0.8945 (ptmt) cc_final: 0.8327 (ttpp) REVERT: G 93 GLN cc_start: 0.8856 (pt0) cc_final: 0.7885 (pp30) REVERT: G 172 TRP cc_start: 0.7403 (t60) cc_final: 0.6293 (m-10) REVERT: G 255 PHE cc_start: 0.8557 (t80) cc_final: 0.8340 (t80) REVERT: H 137 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7077 (mp0) REVERT: H 176 MET cc_start: 0.7234 (tpt) cc_final: 0.6769 (tmm) REVERT: I 159 ILE cc_start: 0.9629 (pt) cc_final: 0.9395 (mt) REVERT: J 51 LEU cc_start: 0.9561 (tp) cc_final: 0.9338 (tp) REVERT: J 57 GLN cc_start: 0.9011 (tm-30) cc_final: 0.8399 (tm-30) REVERT: J 105 ASN cc_start: 0.9008 (OUTLIER) cc_final: 0.8727 (t0) REVERT: J 150 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8934 (tttm) REVERT: K 70 ARG cc_start: 0.8602 (ttt-90) cc_final: 0.8180 (ttp80) REVERT: L 31 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7493 (pp30) REVERT: L 86 ARG cc_start: 0.8761 (ttm110) cc_final: 0.8446 (ttm110) outliers start: 113 outliers final: 74 residues processed: 453 average time/residue: 0.1240 time to fit residues: 84.1310 Evaluate side-chains 410 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 331 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 261 MET Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain J residue 105 ASN Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain J residue 150 LYS Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain L residue 31 GLN Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 87 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 42 optimal weight: 4.9990 chunk 84 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 15 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 174 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 183 optimal weight: 7.9990 chunk 132 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 GLN G 51 GLN ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 ASN I 68 ASN I 86 GLN ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 ASN ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.112923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.083083 restraints weight = 40112.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.083384 restraints weight = 24030.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.084379 restraints weight = 17996.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.084511 restraints weight = 16404.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.084756 restraints weight = 15414.351| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16455 Z= 0.147 Angle : 0.742 10.542 22253 Z= 0.374 Chirality : 0.045 0.253 2692 Planarity : 0.004 0.050 2779 Dihedral : 12.111 98.574 2605 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 6.24 % Allowed : 25.91 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.17), residues: 2092 helix: -0.22 (0.17), residues: 881 sheet: -1.70 (0.30), residues: 280 loop : -2.85 (0.18), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 81 TYR 0.051 0.002 TYR D 40 PHE 0.024 0.002 PHE G 213 TRP 0.008 0.001 TRP H 190 HIS 0.003 0.001 HIS I 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (16442) covalent geometry : angle 0.74233 / 0.37 (22253) hydrogen bonds : bond 0.03963 / 2.75 ( 777) hydrogen bonds : angle 5.26705 / 3.65 ( 2235) Misc. bond : bond 0.00236 / 0.16 ( 13) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 395 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.6738 (OUTLIER) cc_final: 0.6413 (p) REVERT: A 46 PHE cc_start: 0.7306 (m-80) cc_final: 0.6853 (m-80) REVERT: A 48 ASN cc_start: 0.9079 (t0) cc_final: 0.8742 (t0) REVERT: A 111 TYR cc_start: 0.8764 (p90) cc_final: 0.8494 (p90) REVERT: B 19 LEU cc_start: 0.8661 (mt) cc_final: 0.8330 (tt) REVERT: B 40 TYR cc_start: 0.7627 (m-10) cc_final: 0.7389 (m-10) REVERT: B 84 MET cc_start: 0.8584 (pmm) cc_final: 0.8248 (ptt) REVERT: B 85 GLU cc_start: 0.8034 (mp0) cc_final: 0.7626 (mp0) REVERT: C 67 LYS cc_start: 0.9059 (ptpt) cc_final: 0.8745 (ptpt) REVERT: D 84 MET cc_start: 0.8385 (pmm) cc_final: 0.8093 (pmm) REVERT: E 7 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7577 (mt-10) REVERT: E 48 ASN cc_start: 0.8334 (t0) cc_final: 0.7538 (m-40) REVERT: E 146 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7277 (pt) REVERT: F 4 ARG cc_start: 0.7873 (mtt180) cc_final: 0.6786 (ttm110) REVERT: F 47 ASP cc_start: 0.8293 (m-30) cc_final: 0.7793 (t0) REVERT: F 67 LYS cc_start: 0.8862 (ptmt) cc_final: 0.8277 (ttpp) REVERT: F 81 ARG cc_start: 0.7665 (ttp80) cc_final: 0.7187 (ttp80) REVERT: F 131 ASP cc_start: 0.5717 (m-30) cc_final: 0.5459 (m-30) REVERT: G 80 ASN cc_start: 0.7658 (t0) cc_final: 0.7372 (t0) REVERT: G 93 GLN cc_start: 0.8799 (pt0) cc_final: 0.8023 (pp30) REVERT: G 138 MET cc_start: 0.8316 (mpp) cc_final: 0.8092 (mpp) REVERT: G 156 PHE cc_start: 0.8621 (m-80) cc_final: 0.8318 (m-80) REVERT: G 172 TRP cc_start: 0.7424 (t60) cc_final: 0.6317 (m-10) REVERT: H 137 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: H 176 MET cc_start: 0.7107 (tpt) cc_final: 0.6700 (tmm) REVERT: H 224 GLN cc_start: 0.8935 (mm-40) cc_final: 0.8674 (mm-40) REVERT: I 83 MET cc_start: 0.8018 (tpp) cc_final: 0.7736 (tpp) REVERT: I 116 LEU cc_start: 0.8981 (mt) cc_final: 0.8433 (mt) REVERT: I 159 ILE cc_start: 0.9620 (pt) cc_final: 0.9384 (mt) REVERT: I 214 TYR cc_start: 0.8031 (t80) cc_final: 0.7665 (t80) REVERT: J 57 GLN cc_start: 0.9014 (tm-30) cc_final: 0.8461 (tm-30) REVERT: J 105 ASN cc_start: 0.8949 (OUTLIER) cc_final: 0.8635 (t0) REVERT: J 150 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8858 (tttm) REVERT: K 29 ARG cc_start: 0.8351 (tpt90) cc_final: 0.8015 (tpt90) REVERT: K 70 ARG cc_start: 0.8605 (ttt-90) cc_final: 0.8172 (ttp80) outliers start: 106 outliers final: 68 residues processed: 459 average time/residue: 0.1237 time to fit residues: 85.0152 Evaluate side-chains 415 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 342 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 261 MET Chi-restraints excluded: chain H residue 11 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 68 ASN Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 202 SER Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain J residue 105 ASN Chi-restraints excluded: chain J residue 150 LYS Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 87 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 108 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 chunk 82 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 150 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 92 ASN F 133 GLN G 51 GLN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 ASN ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.111520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.081843 restraints weight = 40456.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.082443 restraints weight = 28217.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.083011 restraints weight = 21026.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.083357 restraints weight = 18312.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.083374 restraints weight = 17492.871| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16455 Z= 0.186 Angle : 0.757 10.335 22253 Z= 0.384 Chirality : 0.046 0.265 2692 Planarity : 0.004 0.058 2779 Dihedral : 12.021 98.143 2605 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 6.30 % Allowed : 27.09 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.17), residues: 2092 helix: -0.18 (0.17), residues: 890 sheet: -1.67 (0.29), residues: 287 loop : -2.92 (0.17), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 86 TYR 0.047 0.002 TYR D 40 PHE 0.029 0.002 PHE G 213 TRP 0.009 0.002 TRP G 153 HIS 0.004 0.001 HIS J 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (16442) covalent geometry : angle 0.75732 / 0.38 (22253) hydrogen bonds : bond 0.03995 / 2.78 ( 777) hydrogen bonds : angle 5.25281 / 3.65 ( 2235) Misc. bond : bond 0.00221 / 0.15 ( 13) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 354 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.6877 (OUTLIER) cc_final: 0.6632 (p) REVERT: A 46 PHE cc_start: 0.7471 (m-80) cc_final: 0.6924 (m-80) REVERT: A 48 ASN cc_start: 0.9125 (t0) cc_final: 0.8708 (t0) REVERT: A 111 TYR cc_start: 0.8752 (p90) cc_final: 0.8518 (p90) REVERT: B 19 LEU cc_start: 0.8693 (mt) cc_final: 0.8396 (tt) REVERT: B 40 TYR cc_start: 0.7778 (m-10) cc_final: 0.7477 (m-10) REVERT: B 84 MET cc_start: 0.8439 (pmm) cc_final: 0.8173 (ptt) REVERT: B 85 GLU cc_start: 0.7927 (mp0) cc_final: 0.7473 (mp0) REVERT: B 93 LEU cc_start: 0.8393 (pt) cc_final: 0.8156 (pp) REVERT: B 120 GLU cc_start: 0.7356 (tm-30) cc_final: 0.7115 (tm-30) REVERT: C 18 LEU cc_start: 0.9231 (mp) cc_final: 0.8546 (tp) REVERT: C 67 LYS cc_start: 0.9086 (ptpt) cc_final: 0.8744 (ptpt) REVERT: C 87 ASN cc_start: 0.7749 (m110) cc_final: 0.7494 (m-40) REVERT: E 48 ASN cc_start: 0.8276 (t0) cc_final: 0.7501 (m-40) REVERT: E 83 THR cc_start: 0.7891 (OUTLIER) cc_final: 0.7561 (t) REVERT: E 84 MET cc_start: 0.8047 (ptt) cc_final: 0.7792 (ptm) REVERT: E 146 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7220 (pt) REVERT: F 4 ARG cc_start: 0.7904 (mtt180) cc_final: 0.6761 (ttm110) REVERT: F 47 ASP cc_start: 0.8257 (m-30) cc_final: 0.7779 (t0) REVERT: F 67 LYS cc_start: 0.8849 (ptmt) cc_final: 0.8554 (ptmt) REVERT: F 131 ASP cc_start: 0.5564 (m-30) cc_final: 0.5350 (m-30) REVERT: G 80 ASN cc_start: 0.7721 (t0) cc_final: 0.7427 (t0) REVERT: G 156 PHE cc_start: 0.8689 (m-80) cc_final: 0.8352 (m-80) REVERT: G 172 TRP cc_start: 0.7523 (t60) cc_final: 0.6466 (m-10) REVERT: H 137 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7004 (mp0) REVERT: H 176 MET cc_start: 0.7089 (tpt) cc_final: 0.6631 (tmm) REVERT: H 185 TYR cc_start: 0.7510 (t80) cc_final: 0.7058 (t80) REVERT: I 159 ILE cc_start: 0.9638 (pt) cc_final: 0.9308 (mt) REVERT: J 10 GLU cc_start: 0.6902 (mm-30) cc_final: 0.6197 (tp30) REVERT: J 57 GLN cc_start: 0.9030 (tm-30) cc_final: 0.8460 (tm-30) REVERT: J 105 ASN cc_start: 0.8977 (OUTLIER) cc_final: 0.8636 (t0) REVERT: J 150 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8912 (tttm) REVERT: K 70 ARG cc_start: 0.8586 (ttt-90) cc_final: 0.8161 (ttp80) REVERT: L 85 MET cc_start: 0.9100 (mtp) cc_final: 0.8875 (mtp) outliers start: 107 outliers final: 82 residues processed: 427 average time/residue: 0.1263 time to fit residues: 80.8645 Evaluate side-chains 413 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 325 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 261 MET Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 202 SER Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain J residue 105 ASN Chi-restraints excluded: chain J residue 150 LYS Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 91 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 112 optimal weight: 0.0670 chunk 145 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 199 optimal weight: 20.0000 chunk 47 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 157 optimal weight: 0.8980 chunk 147 optimal weight: 7.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 133 GLN G 93 GLN ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 68 ASN ** J 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.113067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.083513 restraints weight = 40003.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.084911 restraints weight = 25690.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.085698 restraints weight = 18302.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.085513 restraints weight = 15450.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.085623 restraints weight = 15059.504| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16455 Z= 0.146 Angle : 0.761 12.441 22253 Z= 0.384 Chirality : 0.045 0.306 2692 Planarity : 0.004 0.052 2779 Dihedral : 11.588 101.069 2604 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 5.89 % Allowed : 28.15 % Favored : 65.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.17), residues: 2092 helix: -0.04 (0.18), residues: 881 sheet: -1.63 (0.31), residues: 269 loop : -2.83 (0.17), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 37 TYR 0.046 0.002 TYR D 40 PHE 0.023 0.002 PHE G 213 TRP 0.008 0.001 TRP I 66 HIS 0.003 0.001 HIS I 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (16442) covalent geometry : angle 0.76077 / 0.38 (22253) hydrogen bonds : bond 0.03923 / 2.73 ( 777) hydrogen bonds : angle 5.23124 / 3.62 ( 2235) Misc. bond : bond 0.00255 / 0.15 ( 13) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 374 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.6820 (OUTLIER) cc_final: 0.6565 (p) REVERT: A 46 PHE cc_start: 0.7443 (m-80) cc_final: 0.6815 (m-80) REVERT: A 48 ASN cc_start: 0.9119 (t0) cc_final: 0.8688 (t0) REVERT: A 111 TYR cc_start: 0.8698 (p90) cc_final: 0.8475 (p90) REVERT: B 40 TYR cc_start: 0.7717 (m-10) cc_final: 0.7427 (m-10) REVERT: B 67 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8690 (tmmt) REVERT: B 84 MET cc_start: 0.8522 (pmm) cc_final: 0.8196 (ptt) REVERT: B 85 GLU cc_start: 0.7813 (mp0) cc_final: 0.7302 (mp0) REVERT: B 93 LEU cc_start: 0.8360 (pt) cc_final: 0.8061 (pp) REVERT: B 107 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7677 (mm) REVERT: C 18 LEU cc_start: 0.9237 (mp) cc_final: 0.8529 (tp) REVERT: C 67 LYS cc_start: 0.9100 (ptpt) cc_final: 0.8713 (ptpt) REVERT: C 87 ASN cc_start: 0.7712 (m110) cc_final: 0.7460 (m-40) REVERT: D 86 ILE cc_start: 0.5342 (OUTLIER) cc_final: 0.4985 (pp) REVERT: E 7 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7504 (mt-10) REVERT: E 48 ASN cc_start: 0.8412 (t0) cc_final: 0.7543 (m-40) REVERT: E 101 ILE cc_start: 0.9009 (mp) cc_final: 0.8287 (mt) REVERT: E 146 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7228 (pt) REVERT: F 4 ARG cc_start: 0.7865 (mtt180) cc_final: 0.6745 (ttm110) REVERT: G 80 ASN cc_start: 0.7785 (t0) cc_final: 0.7522 (t0) REVERT: G 156 PHE cc_start: 0.8625 (m-80) cc_final: 0.8361 (m-80) REVERT: G 172 TRP cc_start: 0.7404 (t60) cc_final: 0.6430 (m-10) REVERT: H 137 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.6907 (mp0) REVERT: H 176 MET cc_start: 0.7014 (tpt) cc_final: 0.6673 (tmm) REVERT: H 224 GLN cc_start: 0.8941 (mm-40) cc_final: 0.8733 (mm-40) REVERT: H 227 ASP cc_start: 0.8530 (t0) cc_final: 0.8286 (t0) REVERT: I 159 ILE cc_start: 0.9613 (pt) cc_final: 0.9352 (mt) REVERT: I 214 TYR cc_start: 0.7955 (t80) cc_final: 0.7645 (t80) REVERT: J 57 GLN cc_start: 0.9009 (tm-30) cc_final: 0.8490 (tm-30) REVERT: K 70 ARG cc_start: 0.8563 (ttt-90) cc_final: 0.8121 (ttp80) REVERT: L 85 MET cc_start: 0.9096 (mtp) cc_final: 0.8873 (mtp) outliers start: 100 outliers final: 72 residues processed: 443 average time/residue: 0.1236 time to fit residues: 83.0177 Evaluate side-chains 415 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 337 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 202 SER Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 68 ASN Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 91 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 76 optimal weight: 10.0000 chunk 119 optimal weight: 0.0020 chunk 144 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 194 optimal weight: 0.0070 chunk 62 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 149 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 overall best weight: 0.8008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 GLN F 133 GLN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.113665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.084251 restraints weight = 40208.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.084831 restraints weight = 25883.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.085800 restraints weight = 18780.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.085836 restraints weight = 16706.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.085960 restraints weight = 15589.608| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16455 Z= 0.146 Angle : 0.770 12.722 22253 Z= 0.388 Chirality : 0.045 0.257 2692 Planarity : 0.004 0.049 2779 Dihedral : 11.277 102.061 2604 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 5.48 % Allowed : 29.15 % Favored : 65.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.18), residues: 2092 helix: 0.08 (0.18), residues: 871 sheet: -1.79 (0.31), residues: 279 loop : -2.72 (0.17), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 86 TYR 0.045 0.002 TYR D 40 PHE 0.022 0.002 PHE G 255 TRP 0.020 0.002 TRP I 66 HIS 0.004 0.001 HIS J 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (16442) covalent geometry : angle 0.77038 / 0.39 (22253) hydrogen bonds : bond 0.03889 / 2.70 ( 777) hydrogen bonds : angle 5.20258 / 3.60 ( 2235) Misc. bond : bond 0.00243 / 0.14 ( 13) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 373 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.6712 (OUTLIER) cc_final: 0.6491 (p) REVERT: A 48 ASN cc_start: 0.9155 (t0) cc_final: 0.8729 (t0) REVERT: A 111 TYR cc_start: 0.8704 (p90) cc_final: 0.8450 (p90) REVERT: B 40 TYR cc_start: 0.7704 (m-10) cc_final: 0.7375 (m-10) REVERT: B 67 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8667 (tmmt) REVERT: B 84 MET cc_start: 0.8566 (pmm) cc_final: 0.8278 (ptt) REVERT: B 85 GLU cc_start: 0.7660 (mp0) cc_final: 0.7144 (mp0) REVERT: B 93 LEU cc_start: 0.8429 (pt) cc_final: 0.8141 (pp) REVERT: C 18 LEU cc_start: 0.9181 (mp) cc_final: 0.8508 (tp) REVERT: C 67 LYS cc_start: 0.9105 (ptpt) cc_final: 0.8684 (ptpt) REVERT: D 86 ILE cc_start: 0.5124 (OUTLIER) cc_final: 0.4732 (pp) REVERT: E 7 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7504 (mt-10) REVERT: E 48 ASN cc_start: 0.8329 (t0) cc_final: 0.7441 (m-40) REVERT: E 57 LYS cc_start: 0.8672 (mtmm) cc_final: 0.8309 (mtpt) REVERT: E 101 ILE cc_start: 0.8900 (mp) cc_final: 0.8281 (mt) REVERT: E 146 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7242 (pt) REVERT: F 4 ARG cc_start: 0.7886 (mtt180) cc_final: 0.6765 (ttm110) REVERT: F 47 ASP cc_start: 0.8225 (m-30) cc_final: 0.7768 (t0) REVERT: F 131 ASP cc_start: 0.5612 (m-30) cc_final: 0.5375 (m-30) REVERT: G 156 PHE cc_start: 0.8569 (m-80) cc_final: 0.8363 (m-80) REVERT: G 172 TRP cc_start: 0.7356 (t60) cc_final: 0.6426 (m-10) REVERT: G 257 LEU cc_start: 0.8853 (mt) cc_final: 0.8325 (mp) REVERT: H 137 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.6902 (mp0) REVERT: H 224 GLN cc_start: 0.8949 (mm-40) cc_final: 0.8726 (mm-40) REVERT: H 227 ASP cc_start: 0.8508 (t0) cc_final: 0.8275 (t0) REVERT: I 116 LEU cc_start: 0.9001 (mt) cc_final: 0.8562 (mp) REVERT: I 139 GLU cc_start: 0.7947 (tp30) cc_final: 0.7713 (tp30) REVERT: I 159 ILE cc_start: 0.9605 (pt) cc_final: 0.9339 (mt) REVERT: J 57 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8535 (tm-30) REVERT: J 150 LYS cc_start: 0.9213 (tttt) cc_final: 0.8853 (tttm) REVERT: K 37 ARG cc_start: 0.7487 (tmt170) cc_final: 0.6988 (tmt170) REVERT: K 70 ARG cc_start: 0.8570 (ttt-90) cc_final: 0.8122 (ttp80) outliers start: 93 outliers final: 77 residues processed: 441 average time/residue: 0.1250 time to fit residues: 83.5560 Evaluate side-chains 417 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 335 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 202 SER Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 91 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 13 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 127 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 176 optimal weight: 0.0870 chunk 95 optimal weight: 0.1980 chunk 92 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 133 GLN G 205 ASN ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.114555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.085673 restraints weight = 40063.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.086921 restraints weight = 25831.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.087807 restraints weight = 18426.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.087664 restraints weight = 15088.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.087733 restraints weight = 14691.184| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16455 Z= 0.143 Angle : 0.785 12.534 22253 Z= 0.392 Chirality : 0.045 0.248 2692 Planarity : 0.004 0.059 2779 Dihedral : 10.780 103.270 2604 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 5.42 % Allowed : 30.27 % Favored : 64.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.18), residues: 2092 helix: 0.17 (0.18), residues: 872 sheet: -1.96 (0.30), residues: 267 loop : -2.63 (0.18), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 86 TYR 0.032 0.002 TYR D 40 PHE 0.029 0.002 PHE H 156 TRP 0.015 0.001 TRP I 66 HIS 0.004 0.001 HIS G 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (16442) covalent geometry : angle 0.78546 / 0.39 (22253) hydrogen bonds : bond 0.03811 / 2.64 ( 777) hydrogen bonds : angle 5.18496 / 3.59 ( 2235) Misc. bond : bond 0.00202 / 0.13 ( 13) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 365 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.7492 (m-80) cc_final: 0.6857 (m-80) REVERT: A 48 ASN cc_start: 0.9121 (t0) cc_final: 0.8712 (t0) REVERT: A 100 SER cc_start: 0.8291 (m) cc_final: 0.8080 (p) REVERT: A 111 TYR cc_start: 0.8681 (p90) cc_final: 0.8446 (p90) REVERT: B 40 TYR cc_start: 0.7635 (m-10) cc_final: 0.7305 (m-10) REVERT: B 67 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8731 (tmmt) REVERT: B 84 MET cc_start: 0.8528 (pmm) cc_final: 0.8238 (ptt) REVERT: B 85 GLU cc_start: 0.7652 (mp0) cc_final: 0.7167 (mp0) REVERT: B 93 LEU cc_start: 0.8312 (pt) cc_final: 0.8024 (pp) REVERT: C 18 LEU cc_start: 0.9155 (mp) cc_final: 0.8460 (tp) REVERT: C 67 LYS cc_start: 0.9077 (ptpt) cc_final: 0.8631 (ptpt) REVERT: C 84 MET cc_start: 0.7912 (pmm) cc_final: 0.7434 (mpp) REVERT: E 7 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7488 (mt-10) REVERT: E 48 ASN cc_start: 0.8277 (t0) cc_final: 0.7362 (m-40) REVERT: E 57 LYS cc_start: 0.8686 (mtmm) cc_final: 0.8464 (mtpp) REVERT: E 146 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7245 (pt) REVERT: F 4 ARG cc_start: 0.7850 (mtt180) cc_final: 0.6710 (ttm110) REVERT: F 47 ASP cc_start: 0.8177 (m-30) cc_final: 0.7768 (t0) REVERT: F 131 ASP cc_start: 0.5597 (m-30) cc_final: 0.5357 (m-30) REVERT: G 147 ILE cc_start: 0.9387 (OUTLIER) cc_final: 0.9049 (tp) REVERT: G 172 TRP cc_start: 0.7369 (t60) cc_final: 0.6422 (m-10) REVERT: G 184 VAL cc_start: 0.7892 (t) cc_final: 0.7354 (p) REVERT: G 227 ASP cc_start: 0.7922 (t70) cc_final: 0.7613 (t0) REVERT: H 137 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: H 224 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8714 (mm-40) REVERT: H 227 ASP cc_start: 0.8469 (t0) cc_final: 0.8259 (t0) REVERT: I 116 LEU cc_start: 0.8958 (mt) cc_final: 0.8622 (mp) REVERT: I 139 GLU cc_start: 0.7893 (tp30) cc_final: 0.7653 (tp30) REVERT: I 159 ILE cc_start: 0.9584 (pt) cc_final: 0.9344 (mt) REVERT: J 57 GLN cc_start: 0.8977 (tm-30) cc_final: 0.8410 (tm-30) REVERT: J 150 LYS cc_start: 0.9194 (tttt) cc_final: 0.8817 (tttm) REVERT: K 37 ARG cc_start: 0.7271 (tmt170) cc_final: 0.6798 (tmt170) REVERT: K 70 ARG cc_start: 0.8521 (ttt-90) cc_final: 0.8079 (ttp80) REVERT: K 86 ARG cc_start: 0.8828 (ttm110) cc_final: 0.8423 (ttm110) REVERT: L 87 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8610 (mt-10) outliers start: 92 outliers final: 68 residues processed: 431 average time/residue: 0.1216 time to fit residues: 78.6509 Evaluate side-chains 411 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 338 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 1 optimal weight: 0.0670 chunk 5 optimal weight: 20.0000 chunk 142 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 157 optimal weight: 0.1980 chunk 32 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 92 optimal weight: 0.0770 overall best weight: 1.0680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 89 ASN F 133 GLN G 205 ASN H 205 ASN ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.114412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.085596 restraints weight = 39952.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.086311 restraints weight = 28770.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.086962 restraints weight = 21423.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.087111 restraints weight = 17546.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.087167 restraints weight = 16159.809| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16455 Z= 0.152 Angle : 0.807 12.929 22253 Z= 0.401 Chirality : 0.045 0.235 2692 Planarity : 0.004 0.061 2779 Dihedral : 10.476 103.209 2602 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 4.48 % Allowed : 31.39 % Favored : 64.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.18), residues: 2092 helix: 0.20 (0.18), residues: 873 sheet: -1.86 (0.31), residues: 258 loop : -2.60 (0.18), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 86 TYR 0.037 0.002 TYR D 40 PHE 0.048 0.002 PHE G 156 TRP 0.014 0.001 TRP I 66 HIS 0.004 0.001 HIS G 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (16442) covalent geometry : angle 0.80713 / 0.40 (22253) hydrogen bonds : bond 0.03838 / 2.64 ( 777) hydrogen bonds : angle 5.23342 / 3.63 ( 2235) Misc. bond : bond 0.00235 / 0.15 ( 13) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 348 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.9069 (t0) cc_final: 0.8580 (t0) REVERT: A 100 SER cc_start: 0.8402 (m) cc_final: 0.8169 (p) REVERT: B 40 TYR cc_start: 0.7693 (m-10) cc_final: 0.7380 (m-10) REVERT: B 67 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8754 (tmmt) REVERT: B 85 GLU cc_start: 0.7704 (mp0) cc_final: 0.7244 (mp0) REVERT: B 93 LEU cc_start: 0.8284 (pt) cc_final: 0.7997 (pp) REVERT: C 18 LEU cc_start: 0.9151 (mp) cc_final: 0.8413 (tp) REVERT: C 67 LYS cc_start: 0.9066 (ptpt) cc_final: 0.8779 (ptpt) REVERT: E 7 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7509 (mt-10) REVERT: E 48 ASN cc_start: 0.8271 (t0) cc_final: 0.7353 (m-40) REVERT: E 111 TYR cc_start: 0.9229 (p90) cc_final: 0.8996 (p90) REVERT: E 146 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7263 (pt) REVERT: F 4 ARG cc_start: 0.7848 (mtt180) cc_final: 0.6683 (ttm110) REVERT: F 47 ASP cc_start: 0.8234 (m-30) cc_final: 0.7766 (t0) REVERT: F 57 LYS cc_start: 0.8609 (ttpp) cc_final: 0.8129 (ttmm) REVERT: F 131 ASP cc_start: 0.5602 (m-30) cc_final: 0.5364 (m-30) REVERT: G 93 GLN cc_start: 0.8577 (pt0) cc_final: 0.8312 (pt0) REVERT: G 147 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.9013 (tp) REVERT: G 172 TRP cc_start: 0.7404 (t60) cc_final: 0.6477 (m-10) REVERT: G 184 VAL cc_start: 0.7870 (t) cc_final: 0.7348 (p) REVERT: G 227 ASP cc_start: 0.7970 (t70) cc_final: 0.7651 (t0) REVERT: H 137 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.6944 (mp0) REVERT: H 224 GLN cc_start: 0.8968 (mm-40) cc_final: 0.8699 (mm-40) REVERT: I 139 GLU cc_start: 0.7958 (tp30) cc_final: 0.7721 (tp30) REVERT: I 159 ILE cc_start: 0.9586 (pt) cc_final: 0.9311 (mt) REVERT: J 57 GLN cc_start: 0.8989 (tm-30) cc_final: 0.8419 (tm-30) REVERT: J 118 GLU cc_start: 0.8132 (tp30) cc_final: 0.7657 (tp30) REVERT: J 150 LYS cc_start: 0.9199 (tttt) cc_final: 0.8807 (tttm) REVERT: K 37 ARG cc_start: 0.7176 (tmt170) cc_final: 0.6736 (tmt170) REVERT: K 70 ARG cc_start: 0.8500 (ttt-90) cc_final: 0.8028 (ttp80) REVERT: L 87 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8617 (mt-10) outliers start: 76 outliers final: 67 residues processed: 404 average time/residue: 0.1281 time to fit residues: 77.3379 Evaluate side-chains 404 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 332 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain H residue 216 VAL Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 117 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 176 optimal weight: 0.5980 chunk 202 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 154 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 133 GLN ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 ASN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 ASN ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.114742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.085903 restraints weight = 39859.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.086287 restraints weight = 29284.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.087040 restraints weight = 21765.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.087314 restraints weight = 17808.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.087440 restraints weight = 16554.106| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.5336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16455 Z= 0.150 Angle : 0.813 14.889 22253 Z= 0.406 Chirality : 0.045 0.208 2692 Planarity : 0.004 0.048 2779 Dihedral : 10.267 104.151 2602 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 4.36 % Allowed : 32.10 % Favored : 63.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.18), residues: 2092 helix: 0.28 (0.18), residues: 879 sheet: -1.80 (0.30), residues: 262 loop : -2.59 (0.18), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 37 TYR 0.036 0.002 TYR D 40 PHE 0.026 0.002 PHE G 255 TRP 0.014 0.001 TRP I 66 HIS 0.004 0.001 HIS G 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (16442) covalent geometry : angle 0.81349 / 0.41 (22253) hydrogen bonds : bond 0.03797 / 2.61 ( 777) hydrogen bonds : angle 5.19198 / 3.60 ( 2235) Misc. bond : bond 0.00218 / 0.14 ( 13) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2865.24 seconds wall clock time: 50 minutes 29.63 seconds (3029.63 seconds total)