Starting phenix.real_space_refine on Fri Feb 6 05:05:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9crp_45874/02_2026/9crp_45874.cif Found real_map, /net/cci-nas-00/data/ceres_data/9crp_45874/02_2026/9crp_45874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9crp_45874/02_2026/9crp_45874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9crp_45874/02_2026/9crp_45874.map" model { file = "/net/cci-nas-00/data/ceres_data/9crp_45874/02_2026/9crp_45874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9crp_45874/02_2026/9crp_45874.cif" } resolution = 3.2 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= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 554 atoms to isotropic. 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 60 5.49 5 S 68 5.16 5 C 13959 2.51 5 N 3717 2.21 5 O 4389 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22193 Number of models: 1 Model: "" Number of chains: 20 Chain: "M" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 474 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "F" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1945 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 10, 'TRANS': 239} Chain breaks: 4 Chain: "B" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2448 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Chain: "C" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2448 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Chain: "E" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2448 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Chain: "D" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2448 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Chain: "A" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2448 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Chain: "G" Number of atoms: 1692 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 211, 1687 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 211, 1687 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200} Chain breaks: 2 bond proxies already assigned to first conformer: 1722 Chain: "S" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 802 Classifications: {'RNA': 38} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 13, 'rna3p_pur': 12, 'rna3p_pyr': 6} Link IDs: {'rna2p': 19, 'rna3p': 18} Chain: "K" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1013 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 3, 'TRANS': 127} Chain breaks: 1 Chain: "L" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1013 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 3, 'TRANS': 127} Chain breaks: 1 Chain: "H" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1013 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 3, 'TRANS': 127} Chain breaks: 1 Chain: "J" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1013 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 3, 'TRANS': 127} Chain breaks: 1 Chain: "N" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain breaks: 1 Chain: "F" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'TRS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'TRS': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'TRS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'TRS': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'TRS': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'TRS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.94, per 1000 atoms: 0.27 Number of scatterers: 22193 At special positions: 0 Unit cell: (133.48, 127.8, 178.92, 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 68 16.00 P 60 15.00 O 4389 8.00 N 3717 7.00 C 13959 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.01 Conformation dependent library (CDL) restraints added in 1.1 seconds 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4972 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 31 sheets defined 43.3% alpha, 16.8% beta 20 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 2.69 Creating SS restraints... Processing helix chain 'F' and resid 49 through 68 removed outlier: 4.127A pdb=" N LEU F 53 " --> pdb=" O SER F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 78 Processing helix chain 'F' and resid 86 through 94 Processing helix chain 'F' and resid 100 through 113 removed outlier: 4.248A pdb=" N ARG F 105 " --> pdb=" O TYR F 101 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ARG F 106 " --> pdb=" O ASN F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 121 Processing helix chain 'F' and resid 192 through 195 Processing helix chain 'F' and resid 207 through 232 removed outlier: 3.669A pdb=" N LEU F 211 " --> pdb=" O GLY F 207 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ALA F 216 " --> pdb=" O GLU F 212 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LYS F 217 " --> pdb=" O ARG F 213 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU F 226 " --> pdb=" O ALA F 222 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TYR F 227 " --> pdb=" O ILE F 223 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N SER F 228 " --> pdb=" O LYS F 224 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU F 229 " --> pdb=" O ALA F 225 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY F 232 " --> pdb=" O SER F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 285 removed outlier: 4.201A pdb=" N THR F 272 " --> pdb=" O ASP F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 318 removed outlier: 3.501A pdb=" N LEU F 314 " --> pdb=" O THR F 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 69 removed outlier: 4.182A pdb=" N LEU B 53 " --> pdb=" O SER B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 Processing helix chain 'B' and resid 86 through 94 removed outlier: 3.546A pdb=" N LEU B 90 " --> pdb=" O THR B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 102 No H-bonds generated for 'chain 'B' and resid 100 through 102' Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.636A pdb=" N PHE B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 121 Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 214 through 225 Processing helix chain 'B' and resid 225 through 232 removed outlier: 4.414A pdb=" N LEU B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 284 removed outlier: 3.715A pdb=" N THR B 273 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY B 282 " --> pdb=" O GLY B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 320 removed outlier: 3.613A pdb=" N LEU B 314 " --> pdb=" O THR B 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 69 removed outlier: 3.766A pdb=" N ALA C 54 " --> pdb=" O GLY C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 86 through 94 Processing helix chain 'C' and resid 100 through 102 No H-bonds generated for 'chain 'C' and resid 100 through 102' Processing helix chain 'C' and resid 103 through 115 removed outlier: 3.634A pdb=" N LYS C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 121 Processing helix chain 'C' and resid 207 through 214 Processing helix chain 'C' and resid 214 through 232 removed outlier: 3.914A pdb=" N LEU C 226 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TYR C 227 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N SER C 228 " --> pdb=" O LYS C 224 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 285 removed outlier: 3.568A pdb=" N LYS C 279 " --> pdb=" O MET C 275 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLY C 282 " --> pdb=" O GLY C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 320 Processing helix chain 'E' and resid 49 through 67 removed outlier: 4.342A pdb=" N LEU E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS E 67 " --> pdb=" O ASP E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 78 removed outlier: 3.709A pdb=" N GLN E 78 " --> pdb=" O SER E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 94 removed outlier: 3.628A pdb=" N LEU E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 115 removed outlier: 4.213A pdb=" N ARG E 105 " --> pdb=" O TYR E 101 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ARG E 106 " --> pdb=" O ASN E 102 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP E 115 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 121 Processing helix chain 'E' and resid 207 through 226 removed outlier: 4.986A pdb=" N ALA E 216 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LYS E 217 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU E 226 " --> pdb=" O ALA E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 232 Processing helix chain 'E' and resid 269 through 284 removed outlier: 4.582A pdb=" N GLY E 282 " --> pdb=" O GLY E 278 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL E 283 " --> pdb=" O LYS E 279 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU E 284 " --> pdb=" O ALA E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 320 removed outlier: 3.547A pdb=" N LEU E 314 " --> pdb=" O THR E 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 69 removed outlier: 3.595A pdb=" N ALA D 54 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS D 55 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA D 56 " --> pdb=" O ALA D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 78 Processing helix chain 'D' and resid 86 through 94 Processing helix chain 'D' and resid 103 through 115 removed outlier: 3.678A pdb=" N ASP D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 121 Processing helix chain 'D' and resid 207 through 226 removed outlier: 3.528A pdb=" N LEU D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ALA D 216 " --> pdb=" O GLU D 212 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N LYS D 217 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU D 226 " --> pdb=" O ALA D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 232 Processing helix chain 'D' and resid 269 through 285 removed outlier: 3.570A pdb=" N THR D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS D 279 " --> pdb=" O MET D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 320 removed outlier: 3.864A pdb=" N LEU D 314 " --> pdb=" O THR D 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 69 removed outlier: 4.299A pdb=" N LEU A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 67 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 78 removed outlier: 3.769A pdb=" N GLN A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 94 removed outlier: 3.562A pdb=" N LEU A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 192 through 195 removed outlier: 3.698A pdb=" N ILE A 195 " --> pdb=" O GLU A 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 192 through 195' Processing helix chain 'A' and resid 207 through 225 removed outlier: 4.811A pdb=" N ALA A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N LYS A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 removed outlier: 4.141A pdb=" N LEU A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 285 Processing helix chain 'A' and resid 310 through 320 removed outlier: 3.534A pdb=" N LEU A 314 " --> pdb=" O THR A 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 42 Processing helix chain 'G' and resid 61 through 65 removed outlier: 3.689A pdb=" N ARG G 65 " --> pdb=" O TYR G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 138 removed outlier: 3.505A pdb=" N TRP G 138 " --> pdb=" O GLU G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 198 removed outlier: 3.692A pdb=" N ILE G 198 " --> pdb=" O ASN G 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 26 Processing helix chain 'K' and resid 28 through 36 Processing helix chain 'K' and resid 39 through 60 Processing helix chain 'K' and resid 102 through 116 Processing helix chain 'K' and resid 117 through 144 removed outlier: 3.718A pdb=" N ARG K 121 " --> pdb=" O VAL K 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 26 Processing helix chain 'L' and resid 28 through 36 Processing helix chain 'L' and resid 39 through 60 Processing helix chain 'L' and resid 102 through 116 Processing helix chain 'L' and resid 117 through 144 removed outlier: 3.717A pdb=" N ARG L 121 " --> pdb=" O VAL L 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 26 Processing helix chain 'H' and resid 28 through 36 Processing helix chain 'H' and resid 39 through 60 Processing helix chain 'H' and resid 102 through 116 Processing helix chain 'H' and resid 117 through 144 removed outlier: 3.723A pdb=" N ARG H 121 " --> pdb=" O VAL H 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 26 Processing helix chain 'J' and resid 28 through 36 Processing helix chain 'J' and resid 39 through 60 Processing helix chain 'J' and resid 102 through 116 Processing helix chain 'J' and resid 117 through 144 removed outlier: 3.709A pdb=" N ARG J 121 " --> pdb=" O VAL J 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 26 Processing helix chain 'N' and resid 28 through 37 Processing helix chain 'N' and resid 39 through 60 Processing helix chain 'N' and resid 102 through 116 Processing helix chain 'N' and resid 117 through 137 removed outlier: 3.661A pdb=" N ARG N 121 " --> pdb=" O VAL N 117 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 137 through 139 removed outlier: 3.818A pdb=" N SER F 249 " --> pdb=" O ARG F 7 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU F 9 " --> pdb=" O LEU F 247 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N LEU F 247 " --> pdb=" O LEU F 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 29 through 36 Processing sheet with id=AA3, first strand: chain 'F' and resid 123 through 125 removed outlier: 3.613A pdb=" N VAL F 131 " --> pdb=" O TYR F 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 2 through 13 current: chain 'B' and resid 24 through 27 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 24 through 27 current: chain 'B' and resid 174 through 190 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 174 through 190 current: chain 'B' and resid 289 through 295 removed outlier: 4.330A pdb=" N THR B 306 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 36 Processing sheet with id=AA6, first strand: chain 'C' and resid 2 through 8 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 2 through 8 current: chain 'C' and resid 184 through 190 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 184 through 190 current: chain 'C' and resid 290 through 295 removed outlier: 7.843A pdb=" N ALA C 291 " --> pdb=" O THR C 306 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 13 removed outlier: 5.108A pdb=" N ASN C 11 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ALA C 182 " --> pdb=" O ASN C 11 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 18 through 21 removed outlier: 5.740A pdb=" N GLU C 19 " --> pdb=" O LYS C 26 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LYS C 26 " --> pdb=" O GLU C 19 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE C 21 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 29 through 35 Processing sheet with id=AB1, first strand: chain 'C' and resid 123 through 125 Processing sheet with id=AB2, first strand: chain 'E' and resid 2 through 11 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 2 through 11 current: chain 'E' and resid 179 through 190 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 179 through 190 current: chain 'E' and resid 289 through 293 removed outlier: 4.275A pdb=" N THR E 306 " --> pdb=" O ALA E 291 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 18 through 21 removed outlier: 4.551A pdb=" N LYS E 26 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N SER E 20 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU E 24 " --> pdb=" O SER E 20 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 29 through 35 Processing sheet with id=AB5, first strand: chain 'E' and resid 123 through 125 Processing sheet with id=AB6, first strand: chain 'D' and resid 2 through 8 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 2 through 8 current: chain 'D' and resid 184 through 190 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 184 through 190 current: chain 'D' and resid 289 through 295 removed outlier: 3.920A pdb=" N THR D 306 " --> pdb=" O ALA D 291 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 10 through 13 current: chain 'D' and resid 24 through 27 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 24 through 27 current: chain 'D' and resid 174 through 182 No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 29 through 35 Processing sheet with id=AB9, first strand: chain 'D' and resid 123 through 125 Processing sheet with id=AC1, first strand: chain 'A' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2 through 13 current: chain 'A' and resid 24 through 25 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 24 through 25 current: chain 'A' and resid 174 through 182 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 174 through 182 current: chain 'A' and resid 290 through 295 removed outlier: 3.574A pdb=" N THR A 306 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 29 through 35 Processing sheet with id=AC3, first strand: chain 'A' and resid 123 through 125 Processing sheet with id=AC4, first strand: chain 'G' and resid 68 through 73 removed outlier: 6.920A pdb=" N TYR G 3 " --> pdb=" O VAL G 157 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL G 157 " --> pdb=" O TYR G 3 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LYS G 5 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL G 155 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE G 7 " --> pdb=" O GLU G 153 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 78 through 80 Processing sheet with id=AC6, first strand: chain 'G' and resid 161 through 163 removed outlier: 3.533A pdb=" N LYS G 161 " --> pdb=" O GLU G 231 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER G 240 " --> pdb=" O GLU G 228 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N TYR G 230 " --> pdb=" O VAL G 238 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N VAL G 238 " --> pdb=" O TYR G 230 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 166 through 169 Processing sheet with id=AC8, first strand: chain 'G' and resid 173 through 174 Processing sheet with id=AC9, first strand: chain 'K' and resid 63 through 69 Processing sheet with id=AD1, first strand: chain 'L' and resid 63 through 69 Processing sheet with id=AD2, first strand: chain 'H' and resid 63 through 69 Processing sheet with id=AD3, first strand: chain 'J' and resid 63 through 69 Processing sheet with id=AD4, first strand: chain 'N' and resid 63 through 68 946 hydrogen bonds defined for protein. 2718 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 3.89 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6222 1.33 - 1.46: 4799 1.46 - 1.58: 11396 1.58 - 1.71: 119 1.71 - 1.83: 133 Bond restraints: 22669 Sorted by residual: bond pdb=" CZ ARG L 52 " pdb=" NH2 ARG L 52 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 8.88e+00 bond pdb=" CZ ARG K 121 " pdb=" NH2 ARG K 121 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.66e+00 bond pdb=" CZ ARG N 52 " pdb=" NH2 ARG N 52 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.64e+00 bond pdb=" CZ ARG K 111 " pdb=" NH2 ARG K 111 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.58e+00 bond pdb=" CZ ARG K 52 " pdb=" NH2 ARG K 52 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.49e+00 ... (remaining 22664 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 27904 1.23 - 2.45: 2125 2.45 - 3.68: 752 3.68 - 4.91: 69 4.91 - 6.14: 9 Bond angle restraints: 30859 Sorted by residual: angle pdb=" OE1 GLN N 55 " pdb=" CD GLN N 55 " pdb=" NE2 GLN N 55 " ideal model delta sigma weight residual 122.60 118.90 3.70 1.00e+00 1.00e+00 1.37e+01 angle pdb=" C ALA N 123 " pdb=" N GLY N 124 " pdb=" CA GLY N 124 " ideal model delta sigma weight residual 119.98 124.07 -4.09 1.11e+00 8.12e-01 1.36e+01 angle pdb=" C VAL H 117 " pdb=" N TYR H 118 " pdb=" CA TYR H 118 " ideal model delta sigma weight residual 120.38 125.40 -5.02 1.37e+00 5.33e-01 1.34e+01 angle pdb=" CA VAL N 117 " pdb=" CB VAL N 117 " pdb=" CG1 VAL N 117 " ideal model delta sigma weight residual 110.40 116.54 -6.14 1.70e+00 3.46e-01 1.30e+01 angle pdb=" OE1 GLN H 55 " pdb=" CD GLN H 55 " pdb=" NE2 GLN H 55 " ideal model delta sigma weight residual 122.60 119.02 3.58 1.00e+00 1.00e+00 1.28e+01 ... (remaining 30854 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.23: 13276 31.23 - 62.46: 427 62.46 - 93.69: 44 93.69 - 124.92: 1 124.92 - 156.15: 4 Dihedral angle restraints: 13752 sinusoidal: 6003 harmonic: 7749 Sorted by residual: dihedral pdb=" O4' U S 38 " pdb=" C1' U S 38 " pdb=" N1 U S 38 " pdb=" C2 U S 38 " ideal model delta sinusoidal sigma weight residual 232.00 81.78 150.22 1 1.70e+01 3.46e-03 6.21e+01 dihedral pdb=" O4' U S 32 " pdb=" C1' U S 32 " pdb=" N1 U S 32 " pdb=" C2 U S 32 " ideal model delta sinusoidal sigma weight residual 232.00 100.50 131.50 1 1.70e+01 3.46e-03 5.52e+01 dihedral pdb=" O4' U S 2 " pdb=" C1' U S 2 " pdb=" N1 U S 2 " pdb=" C2 U S 2 " ideal model delta sinusoidal sigma weight residual -128.00 -42.54 -85.46 1 1.70e+01 3.46e-03 3.06e+01 ... (remaining 13749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2823 0.052 - 0.105: 520 0.105 - 0.157: 232 0.157 - 0.210: 2 0.210 - 0.262: 9 Chirality restraints: 3586 Sorted by residual: chirality pdb=" CA GLU H 26 " pdb=" N GLU H 26 " pdb=" C GLU H 26 " pdb=" CB GLU H 26 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA GLU L 26 " pdb=" N GLU L 26 " pdb=" C GLU L 26 " pdb=" CB GLU L 26 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA GLU N 26 " pdb=" N GLU N 26 " pdb=" C GLU N 26 " pdb=" CB GLU N 26 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 3583 not shown) Planarity restraints: 3693 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR N 48 " -0.107 2.00e-02 2.50e+03 5.64e-02 6.37e+01 pdb=" CG TYR N 48 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR N 48 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR N 48 " 0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR N 48 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR N 48 " 0.027 2.00e-02 2.50e+03 pdb=" CZ TYR N 48 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR N 48 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 48 " -0.106 2.00e-02 2.50e+03 5.59e-02 6.25e+01 pdb=" CG TYR L 48 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR L 48 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR L 48 " 0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR L 48 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR L 48 " 0.025 2.00e-02 2.50e+03 pdb=" CZ TYR L 48 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR L 48 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 48 " -0.106 2.00e-02 2.50e+03 5.58e-02 6.23e+01 pdb=" CG TYR H 48 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR H 48 " 0.048 2.00e-02 2.50e+03 pdb=" CD2 TYR H 48 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR H 48 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR H 48 " 0.026 2.00e-02 2.50e+03 pdb=" CZ TYR H 48 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 48 " -0.080 2.00e-02 2.50e+03 ... (remaining 3690 not shown) Histogram of nonbonded interaction distances: 0.73 - 1.56: 5 1.56 - 2.40: 65 2.40 - 3.23: 20647 3.23 - 4.07: 52377 4.07 - 4.90: 96262 Warning: very small nonbonded interaction distances. Nonbonded interactions: 169356 Sorted by model distance: nonbonded pdb=" CZ ARG L 133 " pdb=" OE1 GLU H 107 " model vdw 0.731 3.270 nonbonded pdb=" NH1 ARG L 133 " pdb=" CD GLU H 107 " model vdw 0.796 3.350 nonbonded pdb=" NH1 ARG L 133 " pdb=" OE1 GLU H 107 " model vdw 0.841 3.120 nonbonded pdb=" NH2 ARG L 133 " pdb=" OE1 GLU H 107 " model vdw 1.379 3.120 nonbonded pdb=" NH1 ARG L 133 " pdb=" OE2 GLU H 107 " model vdw 1.541 3.120 ... (remaining 169351 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 320) selection = (chain 'B' and resid 1 through 320) selection = chain 'C' selection = (chain 'D' and resid 1 through 320) selection = (chain 'E' and resid 1 through 320) } ncs_group { reference = (chain 'H' and (resid 6 through 68 or resid 80 through 137)) selection = (chain 'J' and (resid 6 through 68 or resid 80 through 137)) selection = (chain 'K' and (resid 6 through 68 or resid 80 through 137)) selection = (chain 'L' and (resid 6 through 68 or resid 80 through 137)) selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.200 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 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 : 0.006 0.040 22669 Z= 0.342 Angle : 0.781 6.136 30859 Z= 0.501 Chirality : 0.050 0.262 3586 Planarity : 0.007 0.089 3693 Dihedral : 14.900 156.146 8780 Min Nonbonded Distance : 0.731 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.31 % Allowed : 0.48 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.16), residues: 2631 helix: 1.52 (0.16), residues: 1056 sheet: 0.34 (0.22), residues: 511 loop : -1.70 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 13 TYR 0.107 0.004 TYR N 48 PHE 0.027 0.002 PHE H 22 TRP 0.008 0.001 TRP G 12 HIS 0.002 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00614 (22669) covalent geometry : angle 0.78123 (30859) hydrogen bonds : bond 0.15379 ( 996) hydrogen bonds : angle 5.49320 ( 2818) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 287 time to evaluate : 0.870 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: F 100 ASP cc_start: 0.8824 (m-30) cc_final: 0.8460 (p0) REVERT: F 119 ASP cc_start: 0.8664 (t0) cc_final: 0.8180 (m-30) REVERT: F 142 MET cc_start: 0.9033 (ttm) cc_final: 0.8695 (tpp) REVERT: F 191 ASP cc_start: 0.8185 (p0) cc_final: 0.7882 (t0) REVERT: F 193 ASP cc_start: 0.9030 (m-30) cc_final: 0.8755 (m-30) REVERT: F 227 TYR cc_start: 0.9196 (t80) cc_final: 0.8622 (t80) REVERT: F 257 PHE cc_start: 0.4195 (p90) cc_final: 0.3803 (p90) REVERT: F 266 ASP cc_start: 0.8465 (m-30) cc_final: 0.8091 (t70) REVERT: F 292 TYR cc_start: 0.7645 (m-80) cc_final: 0.6649 (m-80) REVERT: F 314 LEU cc_start: 0.9000 (tp) cc_final: 0.8790 (tp) REVERT: F 318 LEU cc_start: 0.3428 (mt) cc_final: 0.2819 (mt) REVERT: B 112 MET cc_start: 0.8312 (ttt) cc_final: 0.8077 (ttt) REVERT: B 248 MET cc_start: 0.8090 (mmm) cc_final: 0.7875 (mmt) REVERT: C 112 MET cc_start: 0.8208 (ttt) cc_final: 0.7939 (ttm) REVERT: C 163 PHE cc_start: 0.7899 (t80) cc_final: 0.7661 (t80) REVERT: C 245 MET cc_start: 0.8065 (mtt) cc_final: 0.7823 (mtt) REVERT: E 24 LEU cc_start: 0.8467 (tp) cc_final: 0.8139 (pp) REVERT: E 92 ILE cc_start: 0.8791 (mt) cc_final: 0.8590 (mt) REVERT: E 174 ILE cc_start: 0.8889 (mt) cc_final: 0.8568 (tp) REVERT: E 175 PHE cc_start: 0.9268 (p90) cc_final: 0.9003 (p90) REVERT: E 241 PHE cc_start: 0.7939 (m-80) cc_final: 0.7550 (m-80) REVERT: A 124 MET cc_start: 0.8349 (ttp) cc_final: 0.7531 (ttp) REVERT: A 142 MET cc_start: 0.8515 (ttm) cc_final: 0.8122 (ttm) REVERT: G 113 TYR cc_start: 0.8045 (m-80) cc_final: 0.7618 (m-80) REVERT: L 128 MET cc_start: -0.0307 (tpp) cc_final: -0.3073 (mtt) outliers start: 6 outliers final: 3 residues processed: 292 average time/residue: 0.1938 time to fit residues: 84.0666 Evaluate side-chains 149 residues out of total 2269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 146 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain N residue 117 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.0040 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 0.1980 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 ASN B 16 ASN B 165 ASN C 160 HIS A 154 GLN G 63 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.147656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.092518 restraints weight = 71981.109| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 5.39 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22669 Z= 0.154 Angle : 0.561 8.404 30859 Z= 0.297 Chirality : 0.042 0.207 3586 Planarity : 0.004 0.049 3693 Dihedral : 14.077 162.222 3738 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.84 % Allowed : 6.25 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.16), residues: 2631 helix: 1.97 (0.16), residues: 1076 sheet: 0.66 (0.22), residues: 490 loop : -1.59 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG L 133 TYR 0.024 0.001 TYR L 119 PHE 0.020 0.001 PHE F 186 TRP 0.012 0.001 TRP G 12 HIS 0.003 0.001 HIS C 27 Details of bonding type rmsd covalent geometry : bond 0.00341 (22669) covalent geometry : angle 0.56131 (30859) hydrogen bonds : bond 0.04509 ( 996) hydrogen bonds : angle 4.10341 ( 2818) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.905 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: F 142 MET cc_start: 0.9060 (ttm) cc_final: 0.8672 (tpp) REVERT: F 227 TYR cc_start: 0.8885 (t80) cc_final: 0.8467 (t80) REVERT: F 245 MET cc_start: 0.6053 (ptt) cc_final: 0.4491 (mpp) REVERT: B 99 LYS cc_start: 0.8614 (tppt) cc_final: 0.8362 (tppt) REVERT: B 112 MET cc_start: 0.8036 (ttt) cc_final: 0.7795 (ttt) REVERT: C 124 MET cc_start: 0.7986 (tmm) cc_final: 0.7548 (ttt) REVERT: C 163 PHE cc_start: 0.7915 (t80) cc_final: 0.7626 (m-80) REVERT: E 124 MET cc_start: 0.8159 (tmm) cc_final: 0.7714 (ttp) REVERT: E 174 ILE cc_start: 0.8439 (mt) cc_final: 0.8114 (tp) REVERT: E 241 PHE cc_start: 0.7907 (m-80) cc_final: 0.7484 (m-80) REVERT: D 112 MET cc_start: 0.8927 (mtp) cc_final: 0.8620 (mtp) REVERT: D 124 MET cc_start: 0.8737 (tmm) cc_final: 0.8131 (ttt) REVERT: A 124 MET cc_start: 0.8164 (ttp) cc_final: 0.7382 (ttp) REVERT: A 142 MET cc_start: 0.8652 (ttm) cc_final: 0.8293 (ttm) REVERT: G 166 ARG cc_start: 0.8320 (ttm110) cc_final: 0.7958 (tpp80) REVERT: L 128 MET cc_start: -0.1301 (tpp) cc_final: -0.2907 (mtt) REVERT: N 112 MET cc_start: 0.2988 (tmm) cc_final: 0.1607 (mmp) outliers start: 18 outliers final: 11 residues processed: 173 average time/residue: 0.1660 time to fit residues: 45.0854 Evaluate side-chains 139 residues out of total 2269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 213 optimal weight: 50.0000 chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 206 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 205 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 203 optimal weight: 8.9990 chunk 255 optimal weight: 20.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN C 58 GLN E 214 GLN D 160 HIS D 233 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.145757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.091071 restraints weight = 65196.761| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 5.32 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22669 Z= 0.186 Angle : 0.553 11.549 30859 Z= 0.290 Chirality : 0.042 0.160 3586 Planarity : 0.004 0.044 3693 Dihedral : 14.098 165.116 3737 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.19 % Allowed : 8.32 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.16), residues: 2631 helix: 1.94 (0.16), residues: 1079 sheet: 0.71 (0.22), residues: 489 loop : -1.61 (0.17), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 52 TYR 0.021 0.001 TYR F 269 PHE 0.025 0.002 PHE F 186 TRP 0.010 0.001 TRP G 12 HIS 0.006 0.001 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00432 (22669) covalent geometry : angle 0.55339 (30859) hydrogen bonds : bond 0.04349 ( 996) hydrogen bonds : angle 4.01142 ( 2818) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.834 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: F 227 TYR cc_start: 0.8895 (t80) cc_final: 0.8469 (t80) REVERT: F 245 MET cc_start: 0.5366 (ptt) cc_final: 0.3532 (mpp) REVERT: B 99 LYS cc_start: 0.8796 (tppt) cc_final: 0.8468 (tppt) REVERT: C 124 MET cc_start: 0.8052 (tmm) cc_final: 0.7660 (ttt) REVERT: C 163 PHE cc_start: 0.7956 (t80) cc_final: 0.7644 (m-80) REVERT: E 124 MET cc_start: 0.8103 (tmm) cc_final: 0.7704 (ttp) REVERT: E 241 PHE cc_start: 0.7805 (m-80) cc_final: 0.7406 (m-80) REVERT: D 275 MET cc_start: 0.8317 (tpp) cc_final: 0.7921 (mmt) REVERT: A 124 MET cc_start: 0.8297 (ttp) cc_final: 0.7499 (ttp) REVERT: A 142 MET cc_start: 0.8694 (ttm) cc_final: 0.8367 (ttm) REVERT: L 128 MET cc_start: -0.1214 (tpp) cc_final: -0.2719 (mtm) REVERT: N 112 MET cc_start: 0.2454 (tmm) cc_final: 0.1222 (mmp) outliers start: 26 outliers final: 17 residues processed: 162 average time/residue: 0.1590 time to fit residues: 41.2674 Evaluate side-chains 149 residues out of total 2269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain L residue 117 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 34 optimal weight: 0.0370 chunk 160 optimal weight: 7.9990 chunk 203 optimal weight: 7.9990 chunk 175 optimal weight: 0.9980 chunk 194 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 112 optimal weight: 0.0770 chunk 6 optimal weight: 6.9990 chunk 7 optimal weight: 20.0000 chunk 242 optimal weight: 8.9990 overall best weight: 1.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.146569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.090601 restraints weight = 59326.614| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 4.53 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3400 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3400 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22669 Z= 0.133 Angle : 0.498 12.391 30859 Z= 0.262 Chirality : 0.040 0.154 3586 Planarity : 0.004 0.040 3693 Dihedral : 14.026 171.345 3736 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.01 % Allowed : 9.69 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.16), residues: 2631 helix: 2.03 (0.16), residues: 1078 sheet: 0.64 (0.22), residues: 512 loop : -1.48 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 105 TYR 0.020 0.001 TYR F 269 PHE 0.031 0.001 PHE F 186 TRP 0.009 0.001 TRP G 12 HIS 0.003 0.001 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00304 (22669) covalent geometry : angle 0.49836 (30859) hydrogen bonds : bond 0.03729 ( 996) hydrogen bonds : angle 3.81050 ( 2818) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.937 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: F 227 TYR cc_start: 0.8967 (t80) cc_final: 0.8575 (t80) REVERT: C 124 MET cc_start: 0.7975 (tmm) cc_final: 0.7574 (ttt) REVERT: C 163 PHE cc_start: 0.7953 (t80) cc_final: 0.7605 (m-80) REVERT: E 124 MET cc_start: 0.8206 (tmm) cc_final: 0.7780 (ttp) REVERT: D 260 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7747 (ptp) REVERT: D 275 MET cc_start: 0.8310 (tpp) cc_final: 0.7918 (mmt) REVERT: A 124 MET cc_start: 0.8255 (ttp) cc_final: 0.7421 (ttp) REVERT: A 142 MET cc_start: 0.8747 (ttm) cc_final: 0.8378 (ttm) REVERT: G 68 MET cc_start: 0.7789 (mtp) cc_final: 0.7520 (ttm) REVERT: L 128 MET cc_start: -0.1059 (tpp) cc_final: -0.2373 (mtm) REVERT: N 112 MET cc_start: 0.2137 (tmm) cc_final: 0.1389 (mmp) outliers start: 22 outliers final: 11 residues processed: 156 average time/residue: 0.1485 time to fit residues: 37.8641 Evaluate side-chains 145 residues out of total 2269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 301 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 269 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 25 optimal weight: 0.0980 chunk 177 optimal weight: 0.6980 chunk 156 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 234 optimal weight: 20.0000 chunk 83 optimal weight: 1.9990 chunk 256 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.147674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.091699 restraints weight = 60209.947| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 4.82 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22669 Z= 0.098 Angle : 0.464 12.730 30859 Z= 0.244 Chirality : 0.040 0.148 3586 Planarity : 0.003 0.038 3693 Dihedral : 13.928 174.736 3735 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.01 % Allowed : 10.22 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.17), residues: 2631 helix: 2.26 (0.16), residues: 1077 sheet: 0.63 (0.22), residues: 543 loop : -1.26 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 60 TYR 0.021 0.001 TYR F 269 PHE 0.013 0.001 PHE F 201 TRP 0.010 0.001 TRP G 12 HIS 0.003 0.001 HIS E 55 Details of bonding type rmsd covalent geometry : bond 0.00217 (22669) covalent geometry : angle 0.46354 (30859) hydrogen bonds : bond 0.03336 ( 996) hydrogen bonds : angle 3.63733 ( 2818) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.837 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: F 227 TYR cc_start: 0.8944 (t80) cc_final: 0.8582 (t80) REVERT: F 245 MET cc_start: 0.4437 (ptt) cc_final: 0.4028 (mpp) REVERT: C 124 MET cc_start: 0.7788 (tmm) cc_final: 0.7480 (ttt) REVERT: C 245 MET cc_start: 0.7736 (mtt) cc_final: 0.7365 (mtt) REVERT: E 124 MET cc_start: 0.8056 (tmm) cc_final: 0.7610 (ttp) REVERT: D 8 PHE cc_start: 0.7939 (m-80) cc_final: 0.7736 (m-80) REVERT: D 260 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7726 (ptp) REVERT: D 275 MET cc_start: 0.8272 (tpp) cc_final: 0.8005 (mmt) REVERT: A 124 MET cc_start: 0.8096 (ttp) cc_final: 0.7216 (ttp) REVERT: A 142 MET cc_start: 0.8744 (ttm) cc_final: 0.8255 (ttm) REVERT: G 199 TRP cc_start: 0.7284 (m100) cc_final: 0.6965 (m100) REVERT: L 128 MET cc_start: -0.1073 (tpp) cc_final: -0.2434 (mtm) REVERT: H 47 LEU cc_start: 0.0893 (tp) cc_final: 0.0625 (mt) REVERT: N 112 MET cc_start: 0.2028 (tmm) cc_final: 0.1353 (mmp) outliers start: 22 outliers final: 12 residues processed: 159 average time/residue: 0.1447 time to fit residues: 37.6421 Evaluate side-chains 146 residues out of total 2269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain L residue 63 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 36 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 196 optimal weight: 9.9990 chunk 227 optimal weight: 20.0000 chunk 162 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 203 optimal weight: 8.9990 chunk 240 optimal weight: 30.0000 chunk 197 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 GLN C 58 GLN C 102 ASN C 154 GLN E 58 GLN E 102 ASN D 11 ASN D 58 GLN ** D 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 23 ASN A 295 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.143106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.086909 restraints weight = 60343.350| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 4.83 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 22669 Z= 0.284 Angle : 0.641 13.145 30859 Z= 0.332 Chirality : 0.043 0.161 3586 Planarity : 0.005 0.046 3693 Dihedral : 14.228 170.939 3735 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.76 % Allowed : 10.70 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.16), residues: 2631 helix: 1.76 (0.16), residues: 1082 sheet: 0.62 (0.22), residues: 491 loop : -1.64 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 7 TYR 0.034 0.002 TYR D 141 PHE 0.018 0.002 PHE F 234 TRP 0.004 0.001 TRP G 12 HIS 0.011 0.002 HIS E 160 Details of bonding type rmsd covalent geometry : bond 0.00664 (22669) covalent geometry : angle 0.64063 (30859) hydrogen bonds : bond 0.04922 ( 996) hydrogen bonds : angle 4.11575 ( 2818) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 135 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 227 TYR cc_start: 0.8930 (t80) cc_final: 0.8581 (t80) REVERT: F 245 MET cc_start: 0.4957 (OUTLIER) cc_final: 0.4035 (mpp) REVERT: C 124 MET cc_start: 0.7993 (tmm) cc_final: 0.7609 (ttt) REVERT: C 163 PHE cc_start: 0.8074 (t80) cc_final: 0.7579 (m-80) REVERT: C 245 MET cc_start: 0.8072 (mtt) cc_final: 0.7490 (mtt) REVERT: E 112 MET cc_start: 0.8753 (mtp) cc_final: 0.8392 (mtm) REVERT: E 124 MET cc_start: 0.8140 (tmm) cc_final: 0.7893 (ttp) REVERT: D 103 ASP cc_start: 0.8835 (OUTLIER) cc_final: 0.8437 (t0) REVERT: D 260 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8175 (ptp) REVERT: A 112 MET cc_start: 0.8209 (mmm) cc_final: 0.8007 (mtt) REVERT: A 124 MET cc_start: 0.8404 (ttp) cc_final: 0.7505 (ttp) REVERT: A 142 MET cc_start: 0.8657 (ttm) cc_final: 0.8334 (ttm) REVERT: L 128 MET cc_start: -0.1114 (tpp) cc_final: -0.2404 (mtm) REVERT: N 112 MET cc_start: 0.2062 (tmm) cc_final: 0.1410 (mmp) outliers start: 39 outliers final: 24 residues processed: 161 average time/residue: 0.1269 time to fit residues: 33.8493 Evaluate side-chains 160 residues out of total 2269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 8 PHE Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain N residue 31 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 215 optimal weight: 30.0000 chunk 74 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 121 optimal weight: 0.9980 chunk 261 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 147 optimal weight: 0.7980 chunk 218 optimal weight: 20.0000 chunk 111 optimal weight: 3.9990 chunk 158 optimal weight: 0.0980 chunk 221 optimal weight: 0.0050 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.146555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.097120 restraints weight = 76399.641| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 4.97 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3442 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3442 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22669 Z= 0.101 Angle : 0.485 13.537 30859 Z= 0.254 Chirality : 0.040 0.140 3586 Planarity : 0.003 0.034 3693 Dihedral : 13.981 175.134 3735 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.37 % Allowed : 11.32 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.17), residues: 2631 helix: 2.15 (0.16), residues: 1084 sheet: 0.54 (0.22), residues: 566 loop : -1.31 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 213 TYR 0.019 0.001 TYR F 269 PHE 0.015 0.001 PHE C 159 TRP 0.010 0.001 TRP G 12 HIS 0.002 0.001 HIS E 55 Details of bonding type rmsd covalent geometry : bond 0.00223 (22669) covalent geometry : angle 0.48489 (30859) hydrogen bonds : bond 0.03351 ( 996) hydrogen bonds : angle 3.71118 ( 2818) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.805 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: F 142 MET cc_start: 0.8500 (tmm) cc_final: 0.8176 (tmm) REVERT: F 227 TYR cc_start: 0.8987 (t80) cc_final: 0.8260 (t80) REVERT: F 245 MET cc_start: 0.2978 (ptt) cc_final: 0.1700 (mpp) REVERT: C 96 LYS cc_start: 0.9060 (tmtt) cc_final: 0.8694 (tptp) REVERT: C 124 MET cc_start: 0.7831 (tmm) cc_final: 0.7405 (ttt) REVERT: D 103 ASP cc_start: 0.8956 (OUTLIER) cc_final: 0.8403 (t0) REVERT: D 260 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.8037 (ptp) REVERT: D 275 MET cc_start: 0.8288 (tpp) cc_final: 0.7891 (mmt) REVERT: A 124 MET cc_start: 0.8318 (ttp) cc_final: 0.7431 (ttp) REVERT: A 142 MET cc_start: 0.8770 (ttm) cc_final: 0.8288 (ttm) REVERT: G 199 TRP cc_start: 0.7324 (m100) cc_final: 0.7073 (m100) REVERT: L 128 MET cc_start: -0.0681 (tpp) cc_final: -0.2761 (mtm) REVERT: N 112 MET cc_start: 0.3308 (OUTLIER) cc_final: 0.1954 (mmp) outliers start: 30 outliers final: 18 residues processed: 151 average time/residue: 0.1439 time to fit residues: 35.4552 Evaluate side-chains 151 residues out of total 2269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain N residue 112 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 183 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 224 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 chunk 81 optimal weight: 0.0770 chunk 40 optimal weight: 0.0970 chunk 26 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 196 optimal weight: 0.6980 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.146888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.089744 restraints weight = 60387.875| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 4.88 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3419 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3419 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22669 Z= 0.098 Angle : 0.470 13.620 30859 Z= 0.245 Chirality : 0.039 0.138 3586 Planarity : 0.003 0.034 3693 Dihedral : 13.876 176.872 3735 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.10 % Allowed : 11.71 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.17), residues: 2631 helix: 2.28 (0.16), residues: 1085 sheet: 0.70 (0.22), residues: 572 loop : -1.19 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 182 TYR 0.019 0.001 TYR F 269 PHE 0.018 0.001 PHE F 234 TRP 0.010 0.001 TRP G 12 HIS 0.002 0.001 HIS E 55 Details of bonding type rmsd covalent geometry : bond 0.00218 (22669) covalent geometry : angle 0.47006 (30859) hydrogen bonds : bond 0.03247 ( 996) hydrogen bonds : angle 3.57102 ( 2818) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.727 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: F 227 TYR cc_start: 0.9023 (t80) cc_final: 0.8654 (t80) REVERT: F 245 MET cc_start: 0.4122 (ptt) cc_final: 0.3359 (mpp) REVERT: C 96 LYS cc_start: 0.9025 (tmtt) cc_final: 0.8677 (tptp) REVERT: C 124 MET cc_start: 0.7755 (tmm) cc_final: 0.7369 (ttt) REVERT: C 163 PHE cc_start: 0.7945 (t80) cc_final: 0.7414 (m-10) REVERT: D 103 ASP cc_start: 0.8766 (OUTLIER) cc_final: 0.8282 (t0) REVERT: D 260 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7992 (ptp) REVERT: D 275 MET cc_start: 0.8232 (tpp) cc_final: 0.7863 (mmt) REVERT: A 124 MET cc_start: 0.8214 (ttp) cc_final: 0.7378 (ttp) REVERT: A 142 MET cc_start: 0.8804 (ttm) cc_final: 0.8357 (ttm) REVERT: G 199 TRP cc_start: 0.7300 (m100) cc_final: 0.7033 (m100) REVERT: K 112 MET cc_start: -0.0123 (mtp) cc_final: -0.0437 (mmp) REVERT: L 128 MET cc_start: -0.1025 (tpp) cc_final: -0.2370 (mtm) REVERT: N 56 MET cc_start: 0.4647 (ppp) cc_final: 0.4399 (tpp) REVERT: N 112 MET cc_start: 0.1618 (OUTLIER) cc_final: 0.1242 (mmp) outliers start: 24 outliers final: 15 residues processed: 152 average time/residue: 0.1372 time to fit residues: 34.4983 Evaluate side-chains 150 residues out of total 2269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 186 PHE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain J residue 112 MET Chi-restraints excluded: chain N residue 112 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 37 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 119 optimal weight: 9.9990 chunk 165 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 132 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.145358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.087582 restraints weight = 60090.971| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 4.98 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3369 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3369 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22669 Z= 0.151 Angle : 0.522 13.543 30859 Z= 0.272 Chirality : 0.040 0.138 3586 Planarity : 0.003 0.035 3693 Dihedral : 13.991 176.283 3735 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.01 % Allowed : 11.98 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.17), residues: 2631 helix: 2.15 (0.16), residues: 1079 sheet: 0.58 (0.22), residues: 561 loop : -1.24 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 182 TYR 0.018 0.001 TYR F 269 PHE 0.016 0.001 PHE C 159 TRP 0.007 0.001 TRP G 12 HIS 0.004 0.001 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00350 (22669) covalent geometry : angle 0.52235 (30859) hydrogen bonds : bond 0.03731 ( 996) hydrogen bonds : angle 3.71230 ( 2818) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.716 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: F 227 TYR cc_start: 0.9005 (t80) cc_final: 0.8649 (t80) REVERT: F 245 MET cc_start: 0.4145 (ptt) cc_final: 0.3645 (mpp) REVERT: F 260 MET cc_start: 0.5808 (mtm) cc_final: 0.5491 (mtm) REVERT: C 96 LYS cc_start: 0.9058 (tmtt) cc_final: 0.8681 (tptp) REVERT: C 124 MET cc_start: 0.7888 (tmm) cc_final: 0.7433 (ttt) REVERT: C 163 PHE cc_start: 0.7981 (t80) cc_final: 0.7595 (m-80) REVERT: E 78 GLN cc_start: 0.7827 (mp10) cc_final: 0.7278 (mp10) REVERT: D 103 ASP cc_start: 0.8889 (OUTLIER) cc_final: 0.8338 (t0) REVERT: D 161 VAL cc_start: 0.8608 (p) cc_final: 0.8395 (p) REVERT: D 260 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8109 (ptp) REVERT: A 124 MET cc_start: 0.8266 (ttp) cc_final: 0.7373 (ttp) REVERT: A 142 MET cc_start: 0.8803 (ttm) cc_final: 0.8473 (ttm) REVERT: G 199 TRP cc_start: 0.7362 (m100) cc_final: 0.7084 (m100) REVERT: L 128 MET cc_start: -0.1019 (tpp) cc_final: -0.2311 (mtm) REVERT: N 112 MET cc_start: 0.1893 (OUTLIER) cc_final: 0.1509 (mmp) outliers start: 22 outliers final: 17 residues processed: 153 average time/residue: 0.1410 time to fit residues: 35.6643 Evaluate side-chains 156 residues out of total 2269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain J residue 112 MET Chi-restraints excluded: chain N residue 112 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 87 optimal weight: 2.9990 chunk 187 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 chunk 170 optimal weight: 0.6980 chunk 11 optimal weight: 8.9990 chunk 224 optimal weight: 50.0000 chunk 116 optimal weight: 0.9990 chunk 181 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 chunk 217 optimal weight: 6.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.143683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.088919 restraints weight = 72721.068| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 5.46 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 22669 Z= 0.220 Angle : 0.595 13.541 30859 Z= 0.309 Chirality : 0.042 0.147 3586 Planarity : 0.004 0.044 3693 Dihedral : 14.182 175.909 3735 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.06 % Allowed : 12.11 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.16), residues: 2631 helix: 1.85 (0.16), residues: 1082 sheet: 0.65 (0.22), residues: 500 loop : -1.49 (0.18), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 7 TYR 0.028 0.001 TYR L 94 PHE 0.018 0.002 PHE C 159 TRP 0.004 0.001 TRP G 12 HIS 0.007 0.001 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00514 (22669) covalent geometry : angle 0.59492 (30859) hydrogen bonds : bond 0.04343 ( 996) hydrogen bonds : angle 3.98378 ( 2818) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.743 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: F 227 TYR cc_start: 0.8955 (t80) cc_final: 0.8506 (t80) REVERT: C 96 LYS cc_start: 0.9104 (tmtt) cc_final: 0.8719 (tptp) REVERT: C 124 MET cc_start: 0.8122 (tmm) cc_final: 0.7752 (ttt) REVERT: C 163 PHE cc_start: 0.7985 (t80) cc_final: 0.7572 (m-80) REVERT: E 124 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7661 (ttp) REVERT: D 103 ASP cc_start: 0.8926 (OUTLIER) cc_final: 0.8447 (t0) REVERT: D 260 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8171 (ptp) REVERT: A 124 MET cc_start: 0.8360 (ttp) cc_final: 0.7473 (ttp) REVERT: A 142 MET cc_start: 0.8696 (ttm) cc_final: 0.8353 (ttm) REVERT: G 199 TRP cc_start: 0.7111 (m100) cc_final: 0.6855 (m100) REVERT: L 128 MET cc_start: -0.0799 (tpp) cc_final: -0.2295 (mtm) REVERT: N 112 MET cc_start: 0.2858 (OUTLIER) cc_final: 0.2412 (mmp) outliers start: 23 outliers final: 17 residues processed: 150 average time/residue: 0.1280 time to fit residues: 31.9376 Evaluate side-chains 152 residues out of total 2269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain J residue 112 MET Chi-restraints excluded: chain N residue 112 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 119 optimal weight: 4.9990 chunk 165 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 200 optimal weight: 2.9990 chunk 254 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 250 optimal weight: 30.0000 chunk 174 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 169 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.145969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.088680 restraints weight = 72890.897| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 5.62 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22669 Z= 0.111 Angle : 0.507 13.522 30859 Z= 0.264 Chirality : 0.040 0.145 3586 Planarity : 0.003 0.036 3693 Dihedral : 14.012 176.763 3735 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.92 % Allowed : 12.37 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.17), residues: 2631 helix: 2.05 (0.16), residues: 1084 sheet: 0.54 (0.22), residues: 553 loop : -1.21 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 182 TYR 0.017 0.001 TYR F 269 PHE 0.015 0.001 PHE F 201 TRP 0.009 0.001 TRP G 12 HIS 0.003 0.001 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00252 (22669) covalent geometry : angle 0.50741 (30859) hydrogen bonds : bond 0.03359 ( 996) hydrogen bonds : angle 3.72068 ( 2818) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9987.94 seconds wall clock time: 170 minutes 6.95 seconds (10206.95 seconds total)