Starting phenix.real_space_refine on Thu Feb 5 05:50:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9my3_48725/02_2026/9my3_48725.cif Found real_map, /net/cci-nas-00/data/ceres_data/9my3_48725/02_2026/9my3_48725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9my3_48725/02_2026/9my3_48725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9my3_48725/02_2026/9my3_48725.map" model { file = "/net/cci-nas-00/data/ceres_data/9my3_48725/02_2026/9my3_48725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9my3_48725/02_2026/9my3_48725.cif" } resolution = 3.46 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= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 9728 2.51 5 N 2536 2.21 5 O 2668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 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: 15004 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2718 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 331} Chain breaks: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1033 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 134} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 27 Restraints were copied for chains: C, E, G, D, F, H Time building chain proxies: 2.60, per 1000 atoms: 0.17 Number of scatterers: 15004 At special positions: 0 Unit cell: (110.4, 110.4, 125.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 2668 8.00 N 2536 7.00 C 9728 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: 1.02 Conformation dependent library (CDL) restraints added in 653.0 milliseconds 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3544 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 8 sheets defined 80.3% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 109 through 135 removed outlier: 3.635A pdb=" N PHE A 129 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE A 135 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 168 removed outlier: 3.570A pdb=" N THR A 143 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU A 144 " --> pdb=" O ASN A 140 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A 152 " --> pdb=" O TRP A 148 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 186 through 205 Processing helix chain 'A' and resid 217 through 227 removed outlier: 3.783A pdb=" N PHE A 222 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 225 " --> pdb=" O ARG A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.721A pdb=" N VAL A 231 " --> pdb=" O MET A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 235 through 248 removed outlier: 3.857A pdb=" N SER A 243 " --> pdb=" O ARG A 239 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS A 248 " --> pdb=" O VAL A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 275 removed outlier: 3.605A pdb=" N LEU A 252 " --> pdb=" O HIS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 301 removed outlier: 3.520A pdb=" N THR A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 327 removed outlier: 3.840A pdb=" N VAL A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE A 325 " --> pdb=" O CYS A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 348 Proline residue: A 333 - end of helix removed outlier: 3.876A pdb=" N LYS A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 351 No H-bonds generated for 'chain 'A' and resid 349 through 351' Processing helix chain 'A' and resid 353 through 356 Processing helix chain 'A' and resid 357 through 374 removed outlier: 3.662A pdb=" N ALA A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 384 removed outlier: 3.884A pdb=" N ILE A 384 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 521 removed outlier: 4.348A pdb=" N ALA A 502 " --> pdb=" O HIS A 498 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN A 520 " --> pdb=" O LYS A 516 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 521 " --> pdb=" O LYS A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 554 removed outlier: 3.870A pdb=" N VAL A 530 " --> pdb=" O ASP A 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 21 removed outlier: 4.322A pdb=" N ALA B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 40 removed outlier: 3.504A pdb=" N LEU B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 55 Processing helix chain 'B' and resid 66 through 75 removed outlier: 3.619A pdb=" N ARG B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 92 removed outlier: 4.271A pdb=" N GLU B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 92 " --> pdb=" O GLU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 113 Processing helix chain 'B' and resid 118 through 129 Processing helix chain 'B' and resid 139 through 146 Processing helix chain 'C' and resid 96 through 106 Processing helix chain 'C' and resid 109 through 135 removed outlier: 3.635A pdb=" N PHE C 129 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR C 134 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE C 135 " --> pdb=" O VAL C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 168 removed outlier: 3.570A pdb=" N THR C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU C 144 " --> pdb=" O ASN C 140 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL C 152 " --> pdb=" O TRP C 148 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL C 155 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL C 162 " --> pdb=" O GLY C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 176 through 184 Processing helix chain 'C' and resid 186 through 205 Processing helix chain 'C' and resid 217 through 227 removed outlier: 3.783A pdb=" N PHE C 222 " --> pdb=" O ARG C 218 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 231 removed outlier: 3.721A pdb=" N VAL C 231 " --> pdb=" O MET C 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 228 through 231' Processing helix chain 'C' and resid 235 through 248 removed outlier: 3.857A pdb=" N SER C 243 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS C 248 " --> pdb=" O VAL C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 275 removed outlier: 3.605A pdb=" N LEU C 252 " --> pdb=" O HIS C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 301 removed outlier: 3.520A pdb=" N THR C 301 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 327 removed outlier: 3.840A pdb=" N VAL C 324 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE C 325 " --> pdb=" O CYS C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 348 Proline residue: C 333 - end of helix removed outlier: 3.876A pdb=" N LYS C 348 " --> pdb=" O LYS C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 351 No H-bonds generated for 'chain 'C' and resid 349 through 351' Processing helix chain 'C' and resid 353 through 356 Processing helix chain 'C' and resid 357 through 374 removed outlier: 3.662A pdb=" N ALA C 374 " --> pdb=" O ARG C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 384 removed outlier: 3.884A pdb=" N ILE C 384 " --> pdb=" O THR C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 521 removed outlier: 4.348A pdb=" N ALA C 502 " --> pdb=" O HIS C 498 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN C 520 " --> pdb=" O LYS C 516 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA C 521 " --> pdb=" O LYS C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 554 removed outlier: 3.870A pdb=" N VAL C 530 " --> pdb=" O ASP C 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 21 removed outlier: 4.322A pdb=" N ALA D 16 " --> pdb=" O GLU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 40 removed outlier: 3.504A pdb=" N LEU D 40 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 55 Processing helix chain 'D' and resid 66 through 75 removed outlier: 3.619A pdb=" N ARG D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 92 removed outlier: 4.271A pdb=" N GLU D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 113 Processing helix chain 'D' and resid 118 through 129 Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'E' and resid 96 through 106 Processing helix chain 'E' and resid 109 through 135 removed outlier: 3.635A pdb=" N PHE E 129 " --> pdb=" O ILE E 125 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR E 134 " --> pdb=" O SER E 130 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE E 135 " --> pdb=" O VAL E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 168 removed outlier: 3.570A pdb=" N THR E 143 " --> pdb=" O ASN E 139 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU E 144 " --> pdb=" O ASN E 140 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL E 152 " --> pdb=" O TRP E 148 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL E 155 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL E 162 " --> pdb=" O GLY E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 171 No H-bonds generated for 'chain 'E' and resid 169 through 171' Processing helix chain 'E' and resid 176 through 184 Processing helix chain 'E' and resid 186 through 205 Processing helix chain 'E' and resid 217 through 227 removed outlier: 3.783A pdb=" N PHE E 222 " --> pdb=" O ARG E 218 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE E 225 " --> pdb=" O ARG E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 231 removed outlier: 3.721A pdb=" N VAL E 231 " --> pdb=" O MET E 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 228 through 231' Processing helix chain 'E' and resid 235 through 248 removed outlier: 3.857A pdb=" N SER E 243 " --> pdb=" O ARG E 239 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS E 248 " --> pdb=" O VAL E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 275 removed outlier: 3.605A pdb=" N LEU E 252 " --> pdb=" O HIS E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 301 removed outlier: 3.520A pdb=" N THR E 301 " --> pdb=" O VAL E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 327 removed outlier: 3.840A pdb=" N VAL E 324 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE E 325 " --> pdb=" O CYS E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 348 Proline residue: E 333 - end of helix removed outlier: 3.876A pdb=" N LYS E 348 " --> pdb=" O LYS E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 351 No H-bonds generated for 'chain 'E' and resid 349 through 351' Processing helix chain 'E' and resid 353 through 356 Processing helix chain 'E' and resid 357 through 374 removed outlier: 3.662A pdb=" N ALA E 374 " --> pdb=" O ARG E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 384 removed outlier: 3.884A pdb=" N ILE E 384 " --> pdb=" O THR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 521 removed outlier: 4.348A pdb=" N ALA E 502 " --> pdb=" O HIS E 498 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN E 520 " --> pdb=" O LYS E 516 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA E 521 " --> pdb=" O LYS E 517 " (cutoff:3.500A) Processing helix chain 'E' and resid 526 through 554 removed outlier: 3.870A pdb=" N VAL E 530 " --> pdb=" O ASP E 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 21 removed outlier: 4.322A pdb=" N ALA F 16 " --> pdb=" O GLU F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 40 removed outlier: 3.504A pdb=" N LEU F 40 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 55 Processing helix chain 'F' and resid 66 through 75 removed outlier: 3.619A pdb=" N ARG F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 92 removed outlier: 4.271A pdb=" N GLU F 85 " --> pdb=" O ASP F 81 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL F 92 " --> pdb=" O GLU F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 113 Processing helix chain 'F' and resid 118 through 129 Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'G' and resid 96 through 106 Processing helix chain 'G' and resid 109 through 135 removed outlier: 3.635A pdb=" N PHE G 129 " --> pdb=" O ILE G 125 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR G 134 " --> pdb=" O SER G 130 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE G 135 " --> pdb=" O VAL G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 168 removed outlier: 3.570A pdb=" N THR G 143 " --> pdb=" O ASN G 139 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU G 144 " --> pdb=" O ASN G 140 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL G 152 " --> pdb=" O TRP G 148 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL G 155 " --> pdb=" O ILE G 151 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL G 162 " --> pdb=" O GLY G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 171 No H-bonds generated for 'chain 'G' and resid 169 through 171' Processing helix chain 'G' and resid 176 through 184 Processing helix chain 'G' and resid 186 through 205 Processing helix chain 'G' and resid 217 through 227 removed outlier: 3.783A pdb=" N PHE G 222 " --> pdb=" O ARG G 218 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE G 225 " --> pdb=" O ARG G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 231 removed outlier: 3.721A pdb=" N VAL G 231 " --> pdb=" O MET G 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 228 through 231' Processing helix chain 'G' and resid 235 through 248 removed outlier: 3.857A pdb=" N SER G 243 " --> pdb=" O ARG G 239 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS G 248 " --> pdb=" O VAL G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 275 removed outlier: 3.605A pdb=" N LEU G 252 " --> pdb=" O HIS G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 301 removed outlier: 3.520A pdb=" N THR G 301 " --> pdb=" O VAL G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 327 removed outlier: 3.840A pdb=" N VAL G 324 " --> pdb=" O SER G 320 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE G 325 " --> pdb=" O CYS G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 348 Proline residue: G 333 - end of helix removed outlier: 3.876A pdb=" N LYS G 348 " --> pdb=" O LYS G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 349 through 351 No H-bonds generated for 'chain 'G' and resid 349 through 351' Processing helix chain 'G' and resid 353 through 356 Processing helix chain 'G' and resid 357 through 374 removed outlier: 3.662A pdb=" N ALA G 374 " --> pdb=" O ARG G 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 379 through 384 removed outlier: 3.884A pdb=" N ILE G 384 " --> pdb=" O THR G 381 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 521 removed outlier: 4.348A pdb=" N ALA G 502 " --> pdb=" O HIS G 498 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN G 520 " --> pdb=" O LYS G 516 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA G 521 " --> pdb=" O LYS G 517 " (cutoff:3.500A) Processing helix chain 'G' and resid 526 through 554 removed outlier: 3.870A pdb=" N VAL G 530 " --> pdb=" O ASP G 526 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 21 removed outlier: 4.322A pdb=" N ALA H 16 " --> pdb=" O GLU H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 40 removed outlier: 3.504A pdb=" N LEU H 40 " --> pdb=" O VAL H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 55 Processing helix chain 'H' and resid 66 through 75 removed outlier: 3.619A pdb=" N ARG H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 92 removed outlier: 4.271A pdb=" N GLU H 85 " --> pdb=" O ASP H 81 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 113 Processing helix chain 'H' and resid 118 through 129 Processing helix chain 'H' and resid 139 through 146 Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 28 Processing sheet with id=AA2, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AA3, first strand: chain 'D' and resid 27 through 28 Processing sheet with id=AA4, first strand: chain 'D' and resid 100 through 102 Processing sheet with id=AA5, first strand: chain 'F' and resid 27 through 28 Processing sheet with id=AA6, first strand: chain 'F' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'H' and resid 27 through 28 Processing sheet with id=AA8, first strand: chain 'H' and resid 100 through 102 1005 hydrogen bonds defined for protein. 2967 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.91 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4812 1.35 - 1.46: 3852 1.46 - 1.58: 6540 1.58 - 1.70: 0 1.70 - 1.82: 124 Bond restraints: 15328 Sorted by residual: bond pdb=" CB ASN B 54 " pdb=" CG ASN B 54 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.15e+00 bond pdb=" CB ASN F 54 " pdb=" CG ASN F 54 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.15e+00 bond pdb=" CB ASN D 54 " pdb=" CG ASN D 54 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.15e+00 bond pdb=" CB ASN H 54 " pdb=" CG ASN H 54 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.15e+00 bond pdb=" CA LYS B 116 " pdb=" C LYS B 116 " ideal model delta sigma weight residual 1.532 1.524 0.008 9.60e-03 1.09e+04 7.06e-01 ... (remaining 15323 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 20344 1.80 - 3.59: 348 3.59 - 5.39: 32 5.39 - 7.18: 24 7.18 - 8.98: 8 Bond angle restraints: 20756 Sorted by residual: angle pdb=" C THR A 301 " pdb=" N THR A 302 " pdb=" CA THR A 302 " ideal model delta sigma weight residual 122.08 126.15 -4.07 1.47e+00 4.63e-01 7.67e+00 angle pdb=" C THR C 301 " pdb=" N THR C 302 " pdb=" CA THR C 302 " ideal model delta sigma weight residual 122.08 126.15 -4.07 1.47e+00 4.63e-01 7.67e+00 angle pdb=" C THR E 301 " pdb=" N THR E 302 " pdb=" CA THR E 302 " ideal model delta sigma weight residual 122.08 126.15 -4.07 1.47e+00 4.63e-01 7.67e+00 angle pdb=" C THR G 301 " pdb=" N THR G 302 " pdb=" CA THR G 302 " ideal model delta sigma weight residual 122.08 126.15 -4.07 1.47e+00 4.63e-01 7.67e+00 angle pdb=" CB ARG A 550 " pdb=" CG ARG A 550 " pdb=" CD ARG A 550 " ideal model delta sigma weight residual 111.30 117.28 -5.98 2.30e+00 1.89e-01 6.77e+00 ... (remaining 20751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7944 17.97 - 35.93: 736 35.93 - 53.90: 192 53.90 - 71.86: 48 71.86 - 89.83: 24 Dihedral angle restraints: 8944 sinusoidal: 3444 harmonic: 5500 Sorted by residual: dihedral pdb=" CB GLU C 274 " pdb=" CG GLU C 274 " pdb=" CD GLU C 274 " pdb=" OE1 GLU C 274 " ideal model delta sinusoidal sigma weight residual 0.00 -89.83 89.83 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 274 " pdb=" CG GLU A 274 " pdb=" CD GLU A 274 " pdb=" OE1 GLU A 274 " ideal model delta sinusoidal sigma weight residual 0.00 -89.83 89.83 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU G 274 " pdb=" CG GLU G 274 " pdb=" CD GLU G 274 " pdb=" OE1 GLU G 274 " ideal model delta sinusoidal sigma weight residual 0.00 -89.83 89.83 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 8941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1424 0.028 - 0.057: 624 0.057 - 0.085: 224 0.085 - 0.114: 60 0.114 - 0.142: 12 Chirality restraints: 2344 Sorted by residual: chirality pdb=" CA THR G 302 " pdb=" N THR G 302 " pdb=" C THR G 302 " pdb=" CB THR G 302 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CA THR E 302 " pdb=" N THR E 302 " pdb=" C THR E 302 " pdb=" CB THR E 302 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CA THR C 302 " pdb=" N THR C 302 " pdb=" C THR C 302 " pdb=" CB THR C 302 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 2341 not shown) Planarity restraints: 2612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP C 553 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.95e+00 pdb=" CG ASP C 553 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP C 553 " -0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP C 553 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 553 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.95e+00 pdb=" CG ASP A 553 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP A 553 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP A 553 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP G 553 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.95e+00 pdb=" CG ASP G 553 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP G 553 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP G 553 " 0.014 2.00e-02 2.50e+03 ... (remaining 2609 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 5096 2.85 - 3.36: 15511 3.36 - 3.87: 23428 3.87 - 4.39: 25204 4.39 - 4.90: 43736 Nonbonded interactions: 112975 Sorted by model distance: nonbonded pdb=" OD1 ASN E 355 " pdb=" O ALA H 58 " model vdw 2.337 3.040 nonbonded pdb=" OD1 ASN C 355 " pdb=" O ALA F 58 " model vdw 2.337 3.040 nonbonded pdb=" O ALA B 58 " pdb=" OD1 ASN G 355 " model vdw 2.337 3.040 nonbonded pdb=" OD1 ASN A 355 " pdb=" O ALA D 58 " model vdw 2.338 3.040 nonbonded pdb=" O GLN G 549 " pdb=" OD1 ASP G 553 " model vdw 2.444 3.040 ... (remaining 112970 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.120 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15328 Z= 0.133 Angle : 0.611 8.976 20756 Z= 0.346 Chirality : 0.038 0.142 2344 Planarity : 0.003 0.040 2612 Dihedral : 16.132 89.830 5400 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.52 % Allowed : 15.10 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.19), residues: 1872 helix: 1.81 (0.14), residues: 1356 sheet: None (None), residues: 0 loop : 0.02 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 127 TYR 0.008 0.001 TYR C 115 PHE 0.017 0.001 PHE E 354 TRP 0.014 0.001 TRP G 369 HIS 0.009 0.001 HIS G 230 Details of bonding type rmsd covalent geometry : bond 0.00270 (15328) covalent geometry : angle 0.61113 (20756) hydrogen bonds : bond 0.18941 ( 1005) hydrogen bonds : angle 5.08165 ( 2967) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 272 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7802 (tp30) cc_final: 0.7121 (mm-30) REVERT: B 55 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8616 (mm-30) REVERT: C 105 GLU cc_start: 0.7803 (tp30) cc_final: 0.7122 (mm-30) REVERT: D 55 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8615 (mm-30) REVERT: E 105 GLU cc_start: 0.7805 (tp30) cc_final: 0.7124 (mm-30) REVERT: F 55 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8616 (mm-30) REVERT: G 105 GLU cc_start: 0.7802 (tp30) cc_final: 0.7120 (mm-30) REVERT: H 55 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8614 (mm-30) outliers start: 8 outliers final: 8 residues processed: 272 average time/residue: 0.1129 time to fit residues: 44.9729 Evaluate side-chains 256 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 248 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain G residue 192 ASP Chi-restraints excluded: chain G residue 355 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.0470 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 0.0970 chunk 149 optimal weight: 7.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS A 540 ASN C 230 HIS C 540 ASN E 230 HIS E 540 ASN G 230 HIS G 540 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.102536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.073983 restraints weight = 33352.195| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.95 r_work: 0.2838 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15328 Z= 0.121 Angle : 0.485 6.253 20756 Z= 0.259 Chirality : 0.037 0.155 2344 Planarity : 0.003 0.027 2612 Dihedral : 4.192 45.978 2080 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.56 % Allowed : 14.06 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.19), residues: 1872 helix: 2.30 (0.14), residues: 1376 sheet: None (None), residues: 0 loop : -0.33 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 544 TYR 0.009 0.001 TYR G 115 PHE 0.017 0.001 PHE A 117 TRP 0.010 0.001 TRP G 369 HIS 0.008 0.001 HIS G 230 Details of bonding type rmsd covalent geometry : bond 0.00233 (15328) covalent geometry : angle 0.48457 (20756) hydrogen bonds : bond 0.05340 ( 1005) hydrogen bonds : angle 3.87173 ( 2967) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 280 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 PHE cc_start: 0.8314 (t80) cc_final: 0.8003 (t80) REVERT: B 142 PHE cc_start: 0.8481 (t80) cc_final: 0.8215 (t80) REVERT: C 117 PHE cc_start: 0.8316 (t80) cc_final: 0.8006 (t80) REVERT: D 142 PHE cc_start: 0.8485 (t80) cc_final: 0.8213 (t80) REVERT: E 117 PHE cc_start: 0.8316 (t80) cc_final: 0.8004 (t80) REVERT: F 142 PHE cc_start: 0.8485 (t80) cc_final: 0.8218 (t80) REVERT: G 117 PHE cc_start: 0.8313 (t80) cc_final: 0.8000 (t80) REVERT: H 142 PHE cc_start: 0.8488 (t80) cc_final: 0.8220 (t80) outliers start: 24 outliers final: 12 residues processed: 292 average time/residue: 0.1062 time to fit residues: 46.6911 Evaluate side-chains 260 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 248 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 532 GLU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain E residue 204 CYS Chi-restraints excluded: chain E residue 532 GLU Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 532 GLU Chi-restraints excluded: chain G residue 552 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 123 optimal weight: 0.9990 chunk 171 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 144 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 24 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: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN B 112 ASN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN D 112 ASN ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 ASN F 112 ASN ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 540 ASN H 112 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.098505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.069202 restraints weight = 34134.278| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 3.00 r_work: 0.2742 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15328 Z= 0.220 Angle : 0.558 7.064 20756 Z= 0.296 Chirality : 0.040 0.143 2344 Planarity : 0.003 0.030 2612 Dihedral : 3.393 12.233 2064 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.78 % Allowed : 15.62 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.19), residues: 1872 helix: 2.31 (0.14), residues: 1396 sheet: None (None), residues: 0 loop : -0.58 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 127 TYR 0.013 0.001 TYR H 139 PHE 0.015 0.002 PHE G 117 TRP 0.009 0.001 TRP E 294 HIS 0.006 0.001 HIS E 230 Details of bonding type rmsd covalent geometry : bond 0.00523 (15328) covalent geometry : angle 0.55808 (20756) hydrogen bonds : bond 0.06215 ( 1005) hydrogen bonds : angle 4.02899 ( 2967) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 257 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 PHE cc_start: 0.8291 (t80) cc_final: 0.8002 (t80) REVERT: C 117 PHE cc_start: 0.8287 (t80) cc_final: 0.8002 (t80) REVERT: E 117 PHE cc_start: 0.8286 (t80) cc_final: 0.7999 (t80) REVERT: G 117 PHE cc_start: 0.8291 (t80) cc_final: 0.7997 (t80) outliers start: 12 outliers final: 8 residues processed: 261 average time/residue: 0.1053 time to fit residues: 41.2999 Evaluate side-chains 255 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 247 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 204 CYS Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 204 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 177 optimal weight: 0.1980 chunk 48 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 106 optimal weight: 0.0980 chunk 71 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS A 540 ASN C 95 ASN C 230 HIS C 540 ASN E 230 HIS E 540 ASN G 95 ASN G 230 HIS G 353 HIS G 540 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.102282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.073540 restraints weight = 33628.691| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.05 r_work: 0.2829 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15328 Z= 0.110 Angle : 0.464 6.376 20756 Z= 0.244 Chirality : 0.036 0.123 2344 Planarity : 0.002 0.026 2612 Dihedral : 3.253 11.097 2064 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.43 % Allowed : 14.84 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.80 (0.19), residues: 1872 helix: 2.58 (0.14), residues: 1396 sheet: None (None), residues: 0 loop : -0.41 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 550 TYR 0.009 0.001 TYR E 115 PHE 0.016 0.001 PHE G 117 TRP 0.011 0.001 TRP G 369 HIS 0.006 0.001 HIS E 230 Details of bonding type rmsd covalent geometry : bond 0.00222 (15328) covalent geometry : angle 0.46432 (20756) hydrogen bonds : bond 0.04481 ( 1005) hydrogen bonds : angle 3.62669 ( 2967) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 260 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 PHE cc_start: 0.8210 (t80) cc_final: 0.7912 (t80) REVERT: A 263 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8510 (tp) REVERT: B 142 PHE cc_start: 0.8488 (t80) cc_final: 0.8229 (t80) REVERT: C 117 PHE cc_start: 0.8210 (t80) cc_final: 0.7916 (t80) REVERT: C 263 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8517 (tp) REVERT: D 142 PHE cc_start: 0.8492 (t80) cc_final: 0.8230 (t80) REVERT: E 117 PHE cc_start: 0.8208 (t80) cc_final: 0.7912 (t80) REVERT: E 263 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8527 (tp) REVERT: F 142 PHE cc_start: 0.8490 (t80) cc_final: 0.8229 (t80) REVERT: G 117 PHE cc_start: 0.8207 (t80) cc_final: 0.7910 (t80) REVERT: G 263 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8516 (tp) REVERT: H 142 PHE cc_start: 0.8476 (t80) cc_final: 0.8234 (t80) outliers start: 22 outliers final: 8 residues processed: 278 average time/residue: 0.1055 time to fit residues: 44.1814 Evaluate side-chains 256 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 244 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 532 GLU Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 532 GLU Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 532 GLU Chi-restraints excluded: chain H residue 102 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 86 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 119 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 159 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS A 540 ASN B 112 ASN C 230 HIS C 540 ASN D 112 ASN E 95 ASN E 230 HIS E 540 ASN F 112 ASN G 230 HIS G 540 ASN H 112 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.100716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.071731 restraints weight = 34003.762| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.98 r_work: 0.2798 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15328 Z= 0.126 Angle : 0.462 6.754 20756 Z= 0.245 Chirality : 0.037 0.130 2344 Planarity : 0.003 0.027 2612 Dihedral : 3.137 10.506 2064 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.63 % Allowed : 14.65 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.94 (0.19), residues: 1872 helix: 2.70 (0.14), residues: 1396 sheet: None (None), residues: 0 loop : -0.42 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 550 TYR 0.009 0.001 TYR G 115 PHE 0.015 0.001 PHE A 117 TRP 0.007 0.001 TRP E 369 HIS 0.004 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00285 (15328) covalent geometry : angle 0.46226 (20756) hydrogen bonds : bond 0.04683 ( 1005) hydrogen bonds : angle 3.60880 ( 2967) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 244 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8497 (tp) REVERT: C 263 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8499 (tp) REVERT: E 263 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8510 (tp) REVERT: G 263 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8501 (tp) outliers start: 25 outliers final: 20 residues processed: 257 average time/residue: 0.1133 time to fit residues: 43.1947 Evaluate side-chains 260 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 236 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 532 GLU Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 204 CYS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 532 GLU Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 532 GLU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 102 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 60 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 62 optimal weight: 0.5980 chunk 141 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS A 540 ASN B 112 ASN C 230 HIS C 540 ASN D 112 ASN E 230 HIS E 540 ASN F 112 ASN G 230 HIS G 540 ASN H 112 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.101566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.072502 restraints weight = 33758.608| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.96 r_work: 0.2813 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15328 Z= 0.117 Angle : 0.461 6.706 20756 Z= 0.244 Chirality : 0.036 0.112 2344 Planarity : 0.003 0.027 2612 Dihedral : 3.130 10.628 2064 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.63 % Allowed : 15.04 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.01 (0.19), residues: 1872 helix: 2.75 (0.14), residues: 1396 sheet: None (None), residues: 0 loop : -0.38 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 550 TYR 0.009 0.001 TYR C 115 PHE 0.016 0.001 PHE D 142 TRP 0.008 0.001 TRP A 369 HIS 0.004 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00260 (15328) covalent geometry : angle 0.46088 (20756) hydrogen bonds : bond 0.04405 ( 1005) hydrogen bonds : angle 3.57741 ( 2967) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 241 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8553 (mm) cc_final: 0.8331 (mm) REVERT: A 263 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8533 (tp) REVERT: B 127 ARG cc_start: 0.9275 (mtm-85) cc_final: 0.9020 (mtm-85) REVERT: C 121 LEU cc_start: 0.8556 (mm) cc_final: 0.8333 (mm) REVERT: C 263 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8536 (tp) REVERT: D 127 ARG cc_start: 0.9271 (mtm-85) cc_final: 0.9014 (mtm-85) REVERT: E 121 LEU cc_start: 0.8555 (mm) cc_final: 0.8333 (mm) REVERT: E 263 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8546 (tp) REVERT: F 72 MET cc_start: 0.8313 (tmm) cc_final: 0.8052 (tmm) REVERT: F 127 ARG cc_start: 0.9276 (mtm-85) cc_final: 0.9021 (mtm-85) REVERT: G 121 LEU cc_start: 0.8598 (mm) cc_final: 0.8374 (mm) REVERT: G 263 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8536 (tp) REVERT: H 127 ARG cc_start: 0.9275 (mtm-85) cc_final: 0.9022 (mtm-85) outliers start: 25 outliers final: 20 residues processed: 256 average time/residue: 0.1115 time to fit residues: 42.8237 Evaluate side-chains 261 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 237 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 532 GLU Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain E residue 204 CYS Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 102 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 62 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 76 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS A 540 ASN B 112 ASN C 230 HIS C 540 ASN D 112 ASN E 230 HIS E 540 ASN F 112 ASN G 230 HIS G 540 ASN H 112 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.101271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.072238 restraints weight = 33468.678| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.98 r_work: 0.2804 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15328 Z= 0.120 Angle : 0.458 6.505 20756 Z= 0.242 Chirality : 0.036 0.111 2344 Planarity : 0.002 0.027 2612 Dihedral : 3.088 10.164 2064 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.95 % Allowed : 15.76 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.07 (0.19), residues: 1872 helix: 2.78 (0.14), residues: 1396 sheet: None (None), residues: 0 loop : -0.31 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 550 TYR 0.009 0.001 TYR G 115 PHE 0.019 0.001 PHE A 354 TRP 0.007 0.001 TRP G 369 HIS 0.004 0.001 HIS E 230 Details of bonding type rmsd covalent geometry : bond 0.00271 (15328) covalent geometry : angle 0.45767 (20756) hydrogen bonds : bond 0.04397 ( 1005) hydrogen bonds : angle 3.56486 ( 2967) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 253 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8652 (mm) cc_final: 0.8430 (mm) REVERT: A 251 GLU cc_start: 0.8816 (mp0) cc_final: 0.8452 (mp0) REVERT: A 263 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8481 (tp) REVERT: A 534 TYR cc_start: 0.8627 (t80) cc_final: 0.8416 (t80) REVERT: B 127 ARG cc_start: 0.9318 (mtm-85) cc_final: 0.9045 (mtm-85) REVERT: C 121 LEU cc_start: 0.8656 (mm) cc_final: 0.8434 (mm) REVERT: C 251 GLU cc_start: 0.8810 (mp0) cc_final: 0.8449 (mp0) REVERT: C 263 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8489 (tp) REVERT: D 127 ARG cc_start: 0.9314 (mtm-85) cc_final: 0.9038 (mtm-85) REVERT: E 121 LEU cc_start: 0.8653 (mm) cc_final: 0.8432 (mm) REVERT: E 251 GLU cc_start: 0.8803 (mp0) cc_final: 0.8441 (mp0) REVERT: E 263 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8499 (tp) REVERT: E 534 TYR cc_start: 0.8618 (t80) cc_final: 0.8411 (t80) REVERT: F 127 ARG cc_start: 0.9318 (mtm-85) cc_final: 0.9046 (mtm-85) REVERT: G 121 LEU cc_start: 0.8683 (mm) cc_final: 0.8462 (mm) REVERT: G 251 GLU cc_start: 0.8805 (mp0) cc_final: 0.8440 (mp0) REVERT: G 263 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8492 (tp) REVERT: H 127 ARG cc_start: 0.9319 (mtm-85) cc_final: 0.9047 (mtm-85) outliers start: 30 outliers final: 21 residues processed: 275 average time/residue: 0.1116 time to fit residues: 45.8262 Evaluate side-chains 262 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 237 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 204 CYS Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 102 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 83 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 230 HIS A 540 ASN B 112 ASN C 230 HIS C 540 ASN D 112 ASN E 230 HIS E 540 ASN F 112 ASN G 230 HIS G 540 ASN H 112 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.101720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.072581 restraints weight = 33870.969| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.95 r_work: 0.2813 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15328 Z= 0.120 Angle : 0.468 7.228 20756 Z= 0.247 Chirality : 0.036 0.115 2344 Planarity : 0.002 0.027 2612 Dihedral : 3.110 9.844 2064 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.21 % Allowed : 15.82 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.05 (0.19), residues: 1872 helix: 2.76 (0.14), residues: 1396 sheet: None (None), residues: 0 loop : -0.30 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 550 TYR 0.009 0.001 TYR E 115 PHE 0.008 0.001 PHE B 69 TRP 0.009 0.001 TRP E 369 HIS 0.004 0.001 HIS E 230 Details of bonding type rmsd covalent geometry : bond 0.00272 (15328) covalent geometry : angle 0.46822 (20756) hydrogen bonds : bond 0.04376 ( 1005) hydrogen bonds : angle 3.58839 ( 2967) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 241 time to evaluate : 0.588 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: A 121 LEU cc_start: 0.8762 (mm) cc_final: 0.8547 (mm) REVERT: A 263 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8609 (tp) REVERT: A 534 TYR cc_start: 0.8651 (t80) cc_final: 0.8447 (t80) REVERT: B 127 ARG cc_start: 0.9346 (mtm-85) cc_final: 0.9120 (mtm-85) REVERT: C 121 LEU cc_start: 0.8762 (mm) cc_final: 0.8548 (mm) REVERT: C 263 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8618 (tp) REVERT: D 127 ARG cc_start: 0.9345 (mtm-85) cc_final: 0.9117 (mtm-85) REVERT: E 121 LEU cc_start: 0.8763 (mm) cc_final: 0.8550 (mm) REVERT: E 263 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8624 (tp) REVERT: E 534 TYR cc_start: 0.8649 (t80) cc_final: 0.8446 (t80) REVERT: F 127 ARG cc_start: 0.9346 (mtm-85) cc_final: 0.9119 (mtm-85) REVERT: G 121 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8543 (mm) REVERT: G 263 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8619 (tp) REVERT: H 127 ARG cc_start: 0.9351 (mtm-85) cc_final: 0.9125 (mtm-85) outliers start: 34 outliers final: 23 residues processed: 262 average time/residue: 0.1147 time to fit residues: 44.6752 Evaluate side-chains 265 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 237 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 204 CYS Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 102 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 61 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 128 optimal weight: 0.3980 chunk 75 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 172 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 230 HIS A 540 ASN B 112 ASN C 230 HIS C 540 ASN D 112 ASN E 230 HIS E 540 ASN F 112 ASN G 230 HIS G 540 ASN H 112 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.101731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.072510 restraints weight = 33799.259| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.01 r_work: 0.2802 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15328 Z= 0.127 Angle : 0.491 8.058 20756 Z= 0.261 Chirality : 0.037 0.124 2344 Planarity : 0.002 0.027 2612 Dihedral : 3.126 10.615 2064 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.02 % Allowed : 16.15 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.02 (0.19), residues: 1872 helix: 2.74 (0.14), residues: 1400 sheet: None (None), residues: 0 loop : -0.36 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 550 TYR 0.009 0.001 TYR G 115 PHE 0.008 0.001 PHE F 69 TRP 0.009 0.001 TRP E 369 HIS 0.005 0.001 HIS E 230 Details of bonding type rmsd covalent geometry : bond 0.00290 (15328) covalent geometry : angle 0.49149 (20756) hydrogen bonds : bond 0.04385 ( 1005) hydrogen bonds : angle 3.63186 ( 2967) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 242 time to evaluate : 0.439 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: A 263 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8489 (tp) REVERT: A 356 ARG cc_start: 0.8221 (ptp-110) cc_final: 0.8006 (ptp-110) REVERT: B 127 ARG cc_start: 0.9363 (mtm-85) cc_final: 0.9116 (mtm-85) REVERT: C 263 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8495 (tp) REVERT: C 356 ARG cc_start: 0.8227 (ptp-110) cc_final: 0.8013 (ptp-110) REVERT: D 127 ARG cc_start: 0.9361 (mtm-85) cc_final: 0.9113 (mtm-85) REVERT: E 263 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8507 (tp) REVERT: E 356 ARG cc_start: 0.8229 (ptp-110) cc_final: 0.8016 (ptp-110) REVERT: F 127 ARG cc_start: 0.9364 (mtm-85) cc_final: 0.9117 (mtm-85) REVERT: G 263 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8502 (tp) REVERT: G 356 ARG cc_start: 0.8229 (ptp-110) cc_final: 0.8014 (ptp-110) REVERT: H 127 ARG cc_start: 0.9365 (mtm-85) cc_final: 0.9119 (mtm-85) outliers start: 31 outliers final: 26 residues processed: 260 average time/residue: 0.1243 time to fit residues: 47.1175 Evaluate side-chains 268 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 238 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 204 CYS Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 102 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 52 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 80 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 230 HIS A 540 ASN B 112 ASN C 230 HIS C 540 ASN D 112 ASN E 230 HIS E 540 ASN F 112 ASN G 230 HIS H 112 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.101769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.072605 restraints weight = 33688.884| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.00 r_work: 0.2804 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15328 Z= 0.133 Angle : 0.514 8.544 20756 Z= 0.272 Chirality : 0.038 0.200 2344 Planarity : 0.002 0.027 2612 Dihedral : 3.176 11.735 2064 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.95 % Allowed : 16.86 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.99 (0.20), residues: 1872 helix: 2.73 (0.14), residues: 1400 sheet: None (None), residues: 0 loop : -0.41 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 550 TYR 0.009 0.001 TYR E 115 PHE 0.008 0.001 PHE F 69 TRP 0.008 0.001 TRP C 369 HIS 0.005 0.001 HIS E 230 Details of bonding type rmsd covalent geometry : bond 0.00305 (15328) covalent geometry : angle 0.51445 (20756) hydrogen bonds : bond 0.04482 ( 1005) hydrogen bonds : angle 3.70140 ( 2967) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 246 time to evaluate : 0.509 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: A 95 ASN cc_start: 0.4921 (OUTLIER) cc_final: 0.4719 (p0) REVERT: A 263 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8558 (tp) REVERT: A 356 ARG cc_start: 0.8257 (ptp-110) cc_final: 0.8052 (ptp-110) REVERT: C 263 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8564 (tp) REVERT: C 356 ARG cc_start: 0.8270 (ptp-110) cc_final: 0.8066 (ptp-110) REVERT: E 263 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8571 (tp) REVERT: E 356 ARG cc_start: 0.8274 (ptp-110) cc_final: 0.8071 (ptp-110) REVERT: G 263 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8562 (tp) REVERT: G 356 ARG cc_start: 0.8272 (ptp-110) cc_final: 0.8069 (ptp-110) outliers start: 30 outliers final: 25 residues processed: 264 average time/residue: 0.1226 time to fit residues: 47.0328 Evaluate side-chains 274 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 244 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 204 CYS Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 102 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 124 optimal weight: 0.9980 chunk 177 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 130 optimal weight: 0.6980 chunk 162 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 230 HIS A 540 ASN C 230 HIS C 540 ASN E 230 HIS E 540 ASN G 230 HIS G 540 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.103159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.073775 restraints weight = 33644.208| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.04 r_work: 0.2833 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15328 Z= 0.110 Angle : 0.492 8.545 20756 Z= 0.258 Chirality : 0.037 0.220 2344 Planarity : 0.002 0.026 2612 Dihedral : 3.115 11.178 2064 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.43 % Allowed : 17.45 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.03 (0.19), residues: 1872 helix: 2.75 (0.14), residues: 1400 sheet: None (None), residues: 0 loop : -0.37 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 550 TYR 0.013 0.001 TYR E 534 PHE 0.020 0.001 PHE A 354 TRP 0.010 0.001 TRP E 369 HIS 0.004 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00235 (15328) covalent geometry : angle 0.49203 (20756) hydrogen bonds : bond 0.04030 ( 1005) hydrogen bonds : angle 3.60497 ( 2967) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3079.88 seconds wall clock time: 53 minutes 31.24 seconds (3211.24 seconds total)