Starting phenix.real_space_refine on Sat Jul 4 14:57:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gsn_51552/07_2026/9gsn_51552.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gsn_51552/07_2026/9gsn_51552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gsn_51552/07_2026/9gsn_51552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gsn_51552/07_2026/9gsn_51552.map" model { file = "/net/cci-nas-00/data/ceres_data/9gsn_51552/07_2026/9gsn_51552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gsn_51552/07_2026/9gsn_51552.cif" } resolution = 2.58 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= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 21 5.49 5 S 119 5.16 5 C 13713 2.51 5 N 3696 2.21 5 O 4025 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21574 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3051 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 17, 'TRANS': 367} Chain breaks: 2 Chain: "B" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3051 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 17, 'TRANS': 367} Chain breaks: 2 Chain: "C" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3051 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 17, 'TRANS': 367} Chain breaks: 2 Chain: "D" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3051 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 17, 'TRANS': 367} Chain breaks: 2 Chain: "E" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3051 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 17, 'TRANS': 367} Chain breaks: 2 Chain: "F" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3051 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 17, 'TRANS': 367} Chain breaks: 2 Chain: "G" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3051 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 17, 'TRANS': 367} Chain breaks: 2 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.81, per 1000 atoms: 0.27 Number of scatterers: 21574 At special positions: 0 Unit cell: (142.492, 137.403, 139.584, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 119 16.00 P 21 15.00 O 4025 8.00 N 3696 7.00 C 13713 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=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 964.0 milliseconds 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4998 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 25 sheets defined 48.9% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 54 through 84 removed outlier: 3.959A pdb=" N LEU A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ARG A 81 " --> pdb=" O ARG A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 106 removed outlier: 3.507A pdb=" N ALA A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 197 removed outlier: 4.116A pdb=" N ASP A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP A 186 " --> pdb=" O HIS A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 228 Processing helix chain 'A' and resid 233 through 248 Processing helix chain 'A' and resid 248 through 255 removed outlier: 3.889A pdb=" N TYR A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 255 " --> pdb=" O TRP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 285 Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 320 through 324 removed outlier: 3.713A pdb=" N ALA A 324 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 350 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 390 through 402 Processing helix chain 'A' and resid 406 through 420 Processing helix chain 'A' and resid 424 through 435 Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 446 through 451 Processing helix chain 'B' and resid 53 through 80 removed outlier: 3.760A pdb=" N GLY B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR B 80 " --> pdb=" O SER B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 106 removed outlier: 3.977A pdb=" N ALA B 97 " --> pdb=" O ASP B 93 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TRP B 98 " --> pdb=" O LYS B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.570A pdb=" N ASP B 186 " --> pdb=" O HIS B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 228 Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 248 through 255 removed outlier: 4.024A pdb=" N TYR B 252 " --> pdb=" O ASN B 248 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 285 Processing helix chain 'B' and resid 299 through 308 Processing helix chain 'B' and resid 321 through 324 removed outlier: 3.771A pdb=" N ALA B 324 " --> pdb=" O ILE B 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 321 through 324' Processing helix chain 'B' and resid 341 through 350 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 390 through 402 Processing helix chain 'B' and resid 406 through 420 removed outlier: 3.574A pdb=" N ASP B 420 " --> pdb=" O VAL B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 434 Processing helix chain 'B' and resid 438 through 446 Processing helix chain 'B' and resid 447 through 451 Processing helix chain 'C' and resid 50 through 53 Processing helix chain 'C' and resid 54 through 80 removed outlier: 4.187A pdb=" N LEU C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL C 67 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 106 removed outlier: 3.809A pdb=" N ALA C 97 " --> pdb=" O ASP C 93 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP C 98 " --> pdb=" O LYS C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 196 removed outlier: 3.557A pdb=" N ASP C 185 " --> pdb=" O LYS C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 228 Processing helix chain 'C' and resid 233 through 248 Processing helix chain 'C' and resid 248 through 255 removed outlier: 3.627A pdb=" N TYR C 252 " --> pdb=" O ASN C 248 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER C 253 " --> pdb=" O GLY C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 285 Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 321 through 324 removed outlier: 3.700A pdb=" N ALA C 324 " --> pdb=" O ILE C 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 321 through 324' Processing helix chain 'C' and resid 341 through 350 Processing helix chain 'C' and resid 366 through 370 Processing helix chain 'C' and resid 390 through 402 Processing helix chain 'C' and resid 406 through 420 Processing helix chain 'C' and resid 424 through 434 Processing helix chain 'C' and resid 438 through 446 Processing helix chain 'C' and resid 447 through 451 Processing helix chain 'D' and resid 53 through 80 removed outlier: 3.530A pdb=" N GLY D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 106 removed outlier: 4.032A pdb=" N ALA D 97 " --> pdb=" O ASP D 93 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TRP D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 197 removed outlier: 3.924A pdb=" N ASP D 185 " --> pdb=" O LYS D 181 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP D 186 " --> pdb=" O HIS D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 228 Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 248 through 255 removed outlier: 4.066A pdb=" N TYR D 252 " --> pdb=" O ASN D 248 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG D 255 " --> pdb=" O TRP D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 285 Processing helix chain 'D' and resid 299 through 309 Processing helix chain 'D' and resid 321 through 324 removed outlier: 3.803A pdb=" N ALA D 324 " --> pdb=" O ILE D 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 321 through 324' Processing helix chain 'D' and resid 341 through 350 Processing helix chain 'D' and resid 366 through 370 Processing helix chain 'D' and resid 390 through 402 Processing helix chain 'D' and resid 406 through 419 Processing helix chain 'D' and resid 424 through 435 Processing helix chain 'D' and resid 438 through 446 Processing helix chain 'D' and resid 447 through 451 Processing helix chain 'E' and resid 51 through 54 Processing helix chain 'E' and resid 55 through 79 Processing helix chain 'E' and resid 93 through 106 removed outlier: 3.699A pdb=" N ALA E 97 " --> pdb=" O ASP E 93 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TRP E 98 " --> pdb=" O LYS E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 148 removed outlier: 3.601A pdb=" N GLY E 147 " --> pdb=" O ARG E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 197 removed outlier: 4.318A pdb=" N ASP E 185 " --> pdb=" O LYS E 181 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP E 186 " --> pdb=" O HIS E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 228 Processing helix chain 'E' and resid 233 through 248 Processing helix chain 'E' and resid 248 through 255 removed outlier: 3.684A pdb=" N TYR E 252 " --> pdb=" O ASN E 248 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER E 253 " --> pdb=" O GLY E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 285 Processing helix chain 'E' and resid 299 through 308 Processing helix chain 'E' and resid 321 through 324 removed outlier: 3.824A pdb=" N ALA E 324 " --> pdb=" O ILE E 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 321 through 324' Processing helix chain 'E' and resid 341 through 350 Processing helix chain 'E' and resid 366 through 370 Processing helix chain 'E' and resid 390 through 402 Processing helix chain 'E' and resid 406 through 420 removed outlier: 3.520A pdb=" N ASP E 420 " --> pdb=" O VAL E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 435 Processing helix chain 'E' and resid 438 through 446 Processing helix chain 'E' and resid 447 through 451 Processing helix chain 'F' and resid 50 through 52 No H-bonds generated for 'chain 'F' and resid 50 through 52' Processing helix chain 'F' and resid 53 through 79 removed outlier: 3.739A pdb=" N GLY F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 106 removed outlier: 4.004A pdb=" N ALA F 97 " --> pdb=" O ASP F 93 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP F 98 " --> pdb=" O LYS F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 197 removed outlier: 3.825A pdb=" N ASP F 185 " --> pdb=" O LYS F 181 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP F 186 " --> pdb=" O HIS F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 228 Processing helix chain 'F' and resid 233 through 248 Processing helix chain 'F' and resid 248 through 255 removed outlier: 3.517A pdb=" N ARG F 255 " --> pdb=" O TRP F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 285 Processing helix chain 'F' and resid 299 through 308 Processing helix chain 'F' and resid 321 through 324 removed outlier: 3.762A pdb=" N ALA F 324 " --> pdb=" O ILE F 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 321 through 324' Processing helix chain 'F' and resid 341 through 350 Processing helix chain 'F' and resid 366 through 370 Processing helix chain 'F' and resid 390 through 402 Processing helix chain 'F' and resid 405 through 420 removed outlier: 3.736A pdb=" N LYS F 411 " --> pdb=" O ASP F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 424 through 434 Processing helix chain 'F' and resid 438 through 446 Processing helix chain 'F' and resid 447 through 451 Processing helix chain 'G' and resid 50 through 53 Processing helix chain 'G' and resid 54 through 79 Processing helix chain 'G' and resid 80 through 85 Processing helix chain 'G' and resid 93 through 106 removed outlier: 3.935A pdb=" N ALA G 97 " --> pdb=" O ASP G 93 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TRP G 98 " --> pdb=" O LYS G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 197 removed outlier: 3.662A pdb=" N ASP G 185 " --> pdb=" O LYS G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 228 Processing helix chain 'G' and resid 233 through 248 Processing helix chain 'G' and resid 248 through 256 removed outlier: 3.730A pdb=" N TYR G 252 " --> pdb=" O ASN G 248 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER G 253 " --> pdb=" O GLY G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 285 Processing helix chain 'G' and resid 299 through 309 Processing helix chain 'G' and resid 320 through 324 removed outlier: 3.706A pdb=" N ALA G 324 " --> pdb=" O ILE G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 341 through 350 Processing helix chain 'G' and resid 366 through 370 Processing helix chain 'G' and resid 390 through 402 Processing helix chain 'G' and resid 406 through 420 removed outlier: 3.696A pdb=" N ASP G 420 " --> pdb=" O VAL G 416 " (cutoff:3.500A) Processing helix chain 'G' and resid 424 through 434 Processing helix chain 'G' and resid 438 through 446 Processing helix chain 'G' and resid 447 through 451 Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 91 removed outlier: 3.533A pdb=" N THR A 171 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 135 removed outlier: 3.671A pdb=" N THR G 176 " --> pdb=" O ASP G 86 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL G 172 " --> pdb=" O GLN G 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 202 through 203 Processing sheet with id=AA4, first strand: chain 'A' and resid 212 through 215 removed outlier: 3.538A pdb=" N GLU A 212 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER A 208 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASN A 287 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LEU A 317 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N CYS A 289 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N SER A 314 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N PHE A 361 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU A 316 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N THR A 363 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU A 318 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N TYR A 382 " --> pdb=" O ARG A 260 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLY A 262 " --> pdb=" O TYR A 382 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N VAL A 384 " --> pdb=" O GLY A 262 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU A 264 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 110 through 111 removed outlier: 3.688A pdb=" N THR B 171 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 172 " --> pdb=" O GLN B 90 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU B 87 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N VAL C 116 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ILE B 89 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N THR C 118 " --> pdb=" O ILE B 89 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 115 through 122 Processing sheet with id=AA7, first strand: chain 'B' and resid 202 through 203 Processing sheet with id=AA8, first strand: chain 'B' and resid 213 through 215 removed outlier: 4.093A pdb=" N SER B 208 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N SER B 314 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N PHE B 361 " --> pdb=" O SER B 314 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU B 316 " --> pdb=" O PHE B 361 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N THR B 363 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU B 318 " --> pdb=" O THR B 363 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N TYR B 382 " --> pdb=" O ARG B 260 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY B 262 " --> pdb=" O TYR B 382 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N VAL B 384 " --> pdb=" O GLY B 262 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU B 264 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 172 through 173 removed outlier: 7.138A pdb=" N ILE C 89 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N THR D 118 " --> pdb=" O ILE C 89 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 109 through 111 Processing sheet with id=AB2, first strand: chain 'C' and resid 202 through 203 removed outlier: 3.565A pdb=" N LYS C 220 " --> pdb=" O THR C 203 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 212 through 215 removed outlier: 3.973A pdb=" N SER C 208 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N SER C 314 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N PHE C 361 " --> pdb=" O SER C 314 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU C 316 " --> pdb=" O PHE C 361 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N THR C 363 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU C 318 " --> pdb=" O THR C 363 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 109 through 111 removed outlier: 3.832A pdb=" N VAL D 172 " --> pdb=" O GLN D 90 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU D 87 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N VAL E 116 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE D 89 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 8.903A pdb=" N THR E 118 " --> pdb=" O ILE D 89 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 202 through 203 Processing sheet with id=AB6, first strand: chain 'D' and resid 212 through 215 removed outlier: 3.648A pdb=" N GLU D 212 " --> pdb=" O PHE D 209 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER D 208 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N SER D 314 " --> pdb=" O ILE D 359 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N PHE D 361 " --> pdb=" O SER D 314 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU D 316 " --> pdb=" O PHE D 361 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N THR D 363 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU D 318 " --> pdb=" O THR D 363 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.307A pdb=" N THR E 171 " --> pdb=" O GLU E 155 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU E 155 " --> pdb=" O THR E 171 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 202 through 203 Processing sheet with id=AB9, first strand: chain 'E' and resid 212 through 215 removed outlier: 3.569A pdb=" N GLU E 212 " --> pdb=" O PHE E 209 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER E 208 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ASN E 287 " --> pdb=" O ILE E 315 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU E 317 " --> pdb=" O ASN E 287 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N CYS E 289 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N GLU E 319 " --> pdb=" O CYS E 289 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N SER E 314 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N PHE E 361 " --> pdb=" O SER E 314 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU E 316 " --> pdb=" O PHE E 361 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N THR E 363 " --> pdb=" O LEU E 316 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU E 318 " --> pdb=" O THR E 363 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N TYR E 382 " --> pdb=" O ARG E 260 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY E 262 " --> pdb=" O TYR E 382 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N VAL E 384 " --> pdb=" O GLY E 262 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU E 264 " --> pdb=" O VAL E 384 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 109 through 111 removed outlier: 3.611A pdb=" N TRP F 142 " --> pdb=" O VAL F 110 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR F 171 " --> pdb=" O GLU F 155 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 115 through 123 removed outlier: 4.906A pdb=" N HIS F 123 " --> pdb=" O SER F 127 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N SER F 127 " --> pdb=" O HIS F 123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 202 through 203 Processing sheet with id=AC4, first strand: chain 'F' and resid 212 through 215 removed outlier: 3.699A pdb=" N GLU F 212 " --> pdb=" O PHE F 209 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER F 208 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N SER F 314 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N PHE F 361 " --> pdb=" O SER F 314 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU F 316 " --> pdb=" O PHE F 361 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N THR F 363 " --> pdb=" O LEU F 316 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU F 318 " --> pdb=" O THR F 363 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 109 through 110 removed outlier: 3.876A pdb=" N TRP G 142 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 202 through 203 Processing sheet with id=AC7, first strand: chain 'G' and resid 212 through 215 removed outlier: 3.923A pdb=" N SER G 208 " --> pdb=" O ILE G 290 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N SER G 314 " --> pdb=" O ILE G 359 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N PHE G 361 " --> pdb=" O SER G 314 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU G 316 " --> pdb=" O PHE G 361 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N THR G 363 " --> pdb=" O LEU G 316 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU G 318 " --> pdb=" O THR G 363 " (cutoff:3.500A) 1106 hydrogen bonds defined for protein. 3060 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: 4.40 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 7026 1.37 - 1.51: 6443 1.51 - 1.66: 8357 1.66 - 1.81: 143 1.81 - 1.95: 74 Bond restraints: 22043 Sorted by residual: bond pdb=" O3B AGS E 502 " pdb=" PB AGS E 502 " ideal model delta sigma weight residual 1.673 1.571 0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" O3B AGS C 501 " pdb=" PB AGS C 501 " ideal model delta sigma weight residual 1.673 1.577 0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" O3B AGS A 501 " pdb=" PB AGS A 501 " ideal model delta sigma weight residual 1.673 1.578 0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" O3B AGS B 501 " pdb=" PB AGS B 501 " ideal model delta sigma weight residual 1.673 1.579 0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" O3A AGS F 501 " pdb=" PA AGS F 501 " ideal model delta sigma weight residual 1.664 1.571 0.093 2.00e-02 2.50e+03 2.15e+01 ... (remaining 22038 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 29191 2.55 - 5.10: 485 5.10 - 7.65: 98 7.65 - 10.20: 36 10.20 - 12.76: 10 Bond angle restraints: 29820 Sorted by residual: angle pdb=" CA ARG F 77 " pdb=" CB ARG F 77 " pdb=" CG ARG F 77 " ideal model delta sigma weight residual 114.10 123.81 -9.71 2.00e+00 2.50e-01 2.36e+01 angle pdb=" O1B AGS C 502 " pdb=" PB AGS C 502 " pdb=" O2B AGS C 502 " ideal model delta sigma weight residual 121.53 108.77 12.76 3.00e+00 1.11e-01 1.81e+01 angle pdb=" CA ILE G 73 " pdb=" CB ILE G 73 " pdb=" CG1 ILE G 73 " ideal model delta sigma weight residual 110.40 117.63 -7.23 1.70e+00 3.46e-01 1.81e+01 angle pdb=" CB MET A 160 " pdb=" CG MET A 160 " pdb=" SD MET A 160 " ideal model delta sigma weight residual 112.70 124.93 -12.23 3.00e+00 1.11e-01 1.66e+01 angle pdb=" O1A AGS C 502 " pdb=" PA AGS C 502 " pdb=" O2A AGS C 502 " ideal model delta sigma weight residual 122.09 110.77 11.32 3.00e+00 1.11e-01 1.42e+01 ... (remaining 29815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 12993 35.94 - 71.89: 362 71.89 - 107.83: 37 107.83 - 143.78: 7 143.78 - 179.72: 6 Dihedral angle restraints: 13405 sinusoidal: 5621 harmonic: 7784 Sorted by residual: dihedral pdb=" O2B AGS F 501 " pdb=" O3B AGS F 501 " pdb=" PB AGS F 501 " pdb=" PG AGS F 501 " ideal model delta sinusoidal sigma weight residual 7.37 -172.35 179.72 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O3A AGS F 501 " pdb=" O3B AGS F 501 " pdb=" PB AGS F 501 " pdb=" PG AGS F 501 " ideal model delta sinusoidal sigma weight residual 252.61 73.08 179.53 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O3A AGS E 502 " pdb=" O3B AGS E 502 " pdb=" PB AGS E 502 " pdb=" PG AGS E 502 " ideal model delta sinusoidal sigma weight residual -107.39 67.53 -174.92 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 13402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2804 0.055 - 0.109: 380 0.109 - 0.164: 98 0.164 - 0.218: 1 0.218 - 0.273: 7 Chirality restraints: 3290 Sorted by residual: chirality pdb=" C3' AGS F 501 " pdb=" C2' AGS F 501 " pdb=" C4' AGS F 501 " pdb=" O3' AGS F 501 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C3' AGS C 501 " pdb=" C2' AGS C 501 " pdb=" C4' AGS C 501 " pdb=" O3' AGS C 501 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C3' AGS E 502 " pdb=" C2' AGS E 502 " pdb=" C4' AGS E 502 " pdb=" O3' AGS E 502 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 3287 not shown) Planarity restraints: 3752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 376 " 0.425 9.50e-02 1.11e+02 1.90e-01 2.25e+01 pdb=" NE ARG E 376 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG E 376 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG E 376 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG E 376 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 376 " 0.265 9.50e-02 1.11e+02 1.19e-01 9.03e+00 pdb=" NE ARG C 376 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG C 376 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG C 376 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 376 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 77 " -0.235 9.50e-02 1.11e+02 1.05e-01 7.43e+00 pdb=" NE ARG F 77 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG F 77 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG F 77 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG F 77 " -0.004 2.00e-02 2.50e+03 ... (remaining 3749 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 383 2.65 - 3.21: 21534 3.21 - 3.77: 34343 3.77 - 4.34: 46338 4.34 - 4.90: 76065 Nonbonded interactions: 178663 Sorted by model distance: nonbonded pdb=" OE1 GLU D 319 " pdb=" OG1 THR D 363 " model vdw 2.086 3.040 nonbonded pdb=" OH TYR F 96 " pdb=" OE1 GLU F 170 " model vdw 2.124 3.040 nonbonded pdb=" OE2 GLU A 155 " pdb=" OG1 THR A 171 " model vdw 2.149 3.040 nonbonded pdb=" O MET E 103 " pdb=" NH1 ARG E 109 " model vdw 2.181 3.120 nonbonded pdb=" N GLU B 200 " pdb=" OE1 GLU B 200 " model vdw 2.182 3.120 ... (remaining 178658 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 49 through 453) selection = (chain 'B' and resid 49 through 453) selection = (chain 'C' and resid 49 through 453) selection = chain 'D' selection = (chain 'E' and resid 49 through 453) selection = (chain 'F' and resid 49 through 453) selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.850 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: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.890 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 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 : 0.010 0.893 22050 Z= 0.872 Angle : 0.851 12.755 29820 Z= 0.395 Chirality : 0.043 0.273 3290 Planarity : 0.007 0.190 3752 Dihedral : 17.291 179.720 8407 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.96 % Favored : 96.00 % Rotamer: Outliers : 0.73 % Allowed : 20.33 % Favored : 78.94 % 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: 1.02 (0.17), residues: 2653 helix: 2.09 (0.16), residues: 1232 sheet: -0.61 (0.21), residues: 609 loop : -0.38 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 117 TYR 0.028 0.001 TYR A 51 PHE 0.012 0.001 PHE E 184 TRP 0.008 0.001 TRP A 251 HIS 0.004 0.001 HIS E 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.22 (22043) covalent geometry : angle 0.85120 / 0.39 (29820) hydrogen bonds : bond 0.17402 / 11.90 ( 1106) hydrogen bonds : angle 6.17095 / 4.54 ( 3060) Misc. bond : bond 0.47309 / 31.57 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 207 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8758 (tp40) cc_final: 0.8413 (mt0) REVERT: A 108 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7350 (tp-100) REVERT: C 214 ARG cc_start: 0.8691 (mtm110) cc_final: 0.8374 (mtm180) REVERT: E 82 GLN cc_start: 0.8861 (mt0) cc_final: 0.8163 (mt0) REVERT: E 83 MET cc_start: 0.7156 (tpt) cc_final: 0.6682 (tpp) REVERT: E 445 MET cc_start: 0.9214 (mtm) cc_final: 0.8950 (mtm) REVERT: F 52 PHE cc_start: 0.8707 (m-80) cc_final: 0.8475 (m-80) REVERT: G 51 TYR cc_start: 0.8091 (p90) cc_final: 0.7882 (p90) REVERT: G 82 GLN cc_start: 0.8661 (mt0) cc_final: 0.8338 (mt0) outliers start: 17 outliers final: 14 residues processed: 224 average time/residue: 0.7356 time to fit residues: 184.0713 Evaluate side-chains 212 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 198 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 308 ASN Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain F residue 424 SER Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 394 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 0.0870 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN C 122 GLN ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.068564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.045945 restraints weight = 72151.854| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 3.62 r_work: 0.2670 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22050 Z= 0.140 Angle : 0.601 9.105 29820 Z= 0.300 Chirality : 0.042 0.162 3290 Planarity : 0.005 0.080 3752 Dihedral : 11.751 175.278 3212 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.47 % Favored : 96.49 % Rotamer: Outliers : 2.06 % Allowed : 17.42 % Favored : 80.52 % 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: 1.43 (0.17), residues: 2653 helix: 2.40 (0.16), residues: 1197 sheet: -0.32 (0.21), residues: 595 loop : -0.12 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 117 TYR 0.019 0.001 TYR C 51 PHE 0.016 0.001 PHE A 52 TRP 0.017 0.001 TRP C 251 HIS 0.006 0.001 HIS D 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (22043) covalent geometry : angle 0.60119 / 0.30 (29820) hydrogen bonds : bond 0.03691 / 2.45 ( 1106) hydrogen bonds : angle 4.65969 / 3.39 ( 3060) Misc. bond : bond 0.00238 / 0.15 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 211 time to evaluate : 0.842 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: A 82 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8306 (mm110) REVERT: A 88 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7606 (tm-30) REVERT: A 108 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7272 (tp-100) REVERT: B 90 GLN cc_start: 0.8005 (mp10) cc_final: 0.7803 (mp10) REVERT: B 142 TRP cc_start: 0.8327 (m100) cc_final: 0.8085 (m100) REVERT: C 90 GLN cc_start: 0.8604 (mp10) cc_final: 0.8335 (mp10) REVERT: D 419 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9087 (tm) REVERT: D 445 MET cc_start: 0.9510 (mtm) cc_final: 0.9250 (mtm) REVERT: E 82 GLN cc_start: 0.8666 (mt0) cc_final: 0.8202 (mt0) REVERT: E 83 MET cc_start: 0.7167 (tpt) cc_final: 0.6691 (tpp) REVERT: E 445 MET cc_start: 0.9427 (mtm) cc_final: 0.9124 (mtm) REVERT: F 117 ARG cc_start: 0.9103 (ttm-80) cc_final: 0.8856 (ttm-80) REVERT: G 82 GLN cc_start: 0.8635 (mt0) cc_final: 0.8228 (mt0) REVERT: G 83 MET cc_start: 0.8507 (mmm) cc_final: 0.8261 (tpp) REVERT: G 108 GLN cc_start: 0.7516 (tp-100) cc_final: 0.6902 (tt0) outliers start: 48 outliers final: 17 residues processed: 250 average time/residue: 0.7038 time to fit residues: 196.9694 Evaluate side-chains 209 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 308 ASN Chi-restraints excluded: chain C residue 376 ARG Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 86 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 0.7980 chunk 245 optimal weight: 0.3980 chunk 261 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 219 optimal weight: 7.9990 chunk 76 optimal weight: 30.0000 chunk 93 optimal weight: 0.5980 chunk 125 optimal weight: 9.9990 chunk 200 optimal weight: 10.0000 chunk 228 optimal weight: 8.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN C 122 GLN ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.069013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.046484 restraints weight = 72657.672| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.65 r_work: 0.2690 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22050 Z= 0.114 Angle : 0.566 8.326 29820 Z= 0.279 Chirality : 0.040 0.160 3290 Planarity : 0.004 0.063 3752 Dihedral : 10.729 164.022 3201 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.17 % Favored : 96.80 % Rotamer: Outliers : 2.23 % Allowed : 18.06 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.17), residues: 2653 helix: 2.38 (0.16), residues: 1197 sheet: -0.11 (0.21), residues: 616 loop : -0.03 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 117 TYR 0.011 0.001 TYR C 51 PHE 0.008 0.001 PHE A 99 TRP 0.018 0.001 TRP C 251 HIS 0.003 0.000 HIS D 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (22043) covalent geometry : angle 0.56593 / 0.28 (29820) hydrogen bonds : bond 0.03018 / 2.01 ( 1106) hydrogen bonds : angle 4.36050 / 3.16 ( 3060) Misc. bond : bond 0.00220 / 0.14 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 207 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 MET cc_start: 0.9150 (tpt) cc_final: 0.8849 (tpp) REVERT: A 82 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8387 (mm110) REVERT: A 88 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7619 (tm-30) REVERT: A 108 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7277 (tp-100) REVERT: B 90 GLN cc_start: 0.7795 (mp10) cc_final: 0.7466 (mp10) REVERT: B 425 THR cc_start: 0.9346 (OUTLIER) cc_final: 0.9134 (p) REVERT: C 51 TYR cc_start: 0.7879 (t80) cc_final: 0.7496 (t80) REVERT: C 90 GLN cc_start: 0.8560 (mp10) cc_final: 0.8203 (mp10) REVERT: C 295 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8086 (tm-30) REVERT: D 108 GLN cc_start: 0.7837 (pm20) cc_final: 0.7620 (pm20) REVERT: D 295 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8289 (tm-30) REVERT: D 445 MET cc_start: 0.9474 (mtm) cc_final: 0.9197 (mtm) REVERT: E 82 GLN cc_start: 0.8666 (mt0) cc_final: 0.8015 (mt0) REVERT: E 83 MET cc_start: 0.7176 (tpt) cc_final: 0.6708 (tpp) REVERT: E 117 ARG cc_start: 0.9191 (OUTLIER) cc_final: 0.8947 (pmm-80) REVERT: E 445 MET cc_start: 0.9448 (mtm) cc_final: 0.9158 (mtm) REVERT: F 73 ILE cc_start: 0.9060 (tp) cc_final: 0.8815 (pp) REVERT: F 117 ARG cc_start: 0.9164 (ttm-80) cc_final: 0.8924 (ttm-80) REVERT: F 376 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7142 (ttm-80) REVERT: G 59 MET cc_start: 0.9071 (tpp) cc_final: 0.8855 (OUTLIER) REVERT: G 82 GLN cc_start: 0.8625 (mt0) cc_final: 0.8007 (mt0) REVERT: G 83 MET cc_start: 0.8496 (mmm) cc_final: 0.8251 (tpp) REVERT: G 295 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8151 (tm-30) outliers start: 52 outliers final: 14 residues processed: 249 average time/residue: 0.7385 time to fit residues: 204.9123 Evaluate side-chains 211 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 308 ASN Chi-restraints excluded: chain C residue 376 ARG Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain E residue 117 ARG Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 376 ARG Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 295 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 257 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 242 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 175 optimal weight: 3.9990 chunk 240 optimal weight: 0.0570 chunk 209 optimal weight: 3.9990 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 ASN ** F 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.068409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.045841 restraints weight = 72507.196| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 3.62 r_work: 0.2674 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22050 Z= 0.135 Angle : 0.569 9.448 29820 Z= 0.279 Chirality : 0.040 0.161 3290 Planarity : 0.004 0.063 3752 Dihedral : 10.317 162.936 3198 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.20 % Favored : 96.76 % Rotamer: Outliers : 2.10 % Allowed : 18.75 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.17), residues: 2653 helix: 2.44 (0.16), residues: 1197 sheet: 0.01 (0.21), residues: 616 loop : 0.01 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 214 TYR 0.019 0.001 TYR A 80 PHE 0.010 0.001 PHE A 99 TRP 0.016 0.001 TRP C 251 HIS 0.002 0.001 HIS B 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (22043) covalent geometry : angle 0.56864 / 0.28 (29820) hydrogen bonds : bond 0.02952 / 1.96 ( 1106) hydrogen bonds : angle 4.23957 / 3.08 ( 3060) Misc. bond : bond 0.00189 / 0.12 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 199 time to evaluate : 0.813 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: A 59 MET cc_start: 0.9150 (tpt) cc_final: 0.8856 (tpp) REVERT: A 88 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7708 (tm-30) REVERT: A 108 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7293 (tp-100) REVERT: A 117 ARG cc_start: 0.9112 (ttm-80) cc_final: 0.8815 (ttm-80) REVERT: B 83 MET cc_start: 0.8388 (mmm) cc_final: 0.8178 (mmm) REVERT: B 90 GLN cc_start: 0.7814 (mp10) cc_final: 0.7303 (mp10) REVERT: B 425 THR cc_start: 0.9367 (OUTLIER) cc_final: 0.9159 (p) REVERT: C 51 TYR cc_start: 0.7898 (t80) cc_final: 0.7543 (t80) REVERT: C 90 GLN cc_start: 0.8572 (mp10) cc_final: 0.8108 (mp10) REVERT: C 176 THR cc_start: 0.9034 (OUTLIER) cc_final: 0.8553 (p) REVERT: C 434 MET cc_start: 0.9405 (OUTLIER) cc_final: 0.8738 (mpp) REVERT: C 445 MET cc_start: 0.9472 (mtp) cc_final: 0.9100 (mtm) REVERT: D 445 MET cc_start: 0.9490 (mtm) cc_final: 0.9232 (mtm) REVERT: E 82 GLN cc_start: 0.8665 (mt0) cc_final: 0.8191 (mt0) REVERT: E 83 MET cc_start: 0.7157 (tpt) cc_final: 0.6694 (tpp) REVERT: E 117 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.8943 (pmm-80) REVERT: E 295 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8194 (tm-30) REVERT: E 399 MET cc_start: 0.9480 (mmm) cc_final: 0.9269 (mmm) REVERT: E 445 MET cc_start: 0.9428 (mtm) cc_final: 0.9134 (mtm) REVERT: F 73 ILE cc_start: 0.9052 (tp) cc_final: 0.8811 (pp) REVERT: F 117 ARG cc_start: 0.9169 (ttm-80) cc_final: 0.8922 (ttm-80) REVERT: G 59 MET cc_start: 0.9064 (tpp) cc_final: 0.8862 (tpp) REVERT: G 82 GLN cc_start: 0.8604 (mt0) cc_final: 0.7975 (mt0) REVERT: G 83 MET cc_start: 0.8487 (mmm) cc_final: 0.8226 (tpp) REVERT: G 155 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7902 (pp20) outliers start: 49 outliers final: 19 residues processed: 240 average time/residue: 0.6961 time to fit residues: 186.5522 Evaluate side-chains 216 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 308 ASN Chi-restraints excluded: chain C residue 376 ARG Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 117 ARG Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain E residue 308 ASN Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 434 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 122 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 1 optimal weight: 30.0000 chunk 24 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 187 optimal weight: 0.2980 chunk 92 optimal weight: 0.2980 chunk 180 optimal weight: 8.9990 chunk 145 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN B 429 GLN C 122 GLN C 182 HIS ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 HIS ** F 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.067469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.044673 restraints weight = 72881.145| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 3.66 r_work: 0.2631 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 22050 Z= 0.197 Angle : 0.600 8.664 29820 Z= 0.295 Chirality : 0.041 0.162 3290 Planarity : 0.004 0.074 3752 Dihedral : 10.199 172.635 3198 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.28 % Favored : 96.68 % Rotamer: Outliers : 2.15 % Allowed : 19.86 % Favored : 77.99 % 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: 1.66 (0.17), residues: 2653 helix: 2.46 (0.16), residues: 1197 sheet: 0.05 (0.21), residues: 616 loop : 0.02 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 156 TYR 0.022 0.001 TYR E 178 PHE 0.014 0.001 PHE B 276 TRP 0.017 0.001 TRP B 142 HIS 0.002 0.001 HIS A 440 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 (22043) covalent geometry : angle 0.60034 / 0.29 (29820) hydrogen bonds : bond 0.03131 / 2.08 ( 1106) hydrogen bonds : angle 4.21377 / 3.06 ( 3060) Misc. bond : bond 0.00241 / 0.15 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 195 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 MET cc_start: 0.9148 (tpt) cc_final: 0.8880 (tpp) REVERT: A 88 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7544 (tm-30) REVERT: A 90 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7950 (pm20) REVERT: A 108 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7700 (tp-100) REVERT: B 83 MET cc_start: 0.8385 (mmm) cc_final: 0.8135 (mmm) REVERT: B 90 GLN cc_start: 0.7844 (mp10) cc_final: 0.7287 (mp10) REVERT: B 425 THR cc_start: 0.9386 (OUTLIER) cc_final: 0.9166 (p) REVERT: C 51 TYR cc_start: 0.7919 (t80) cc_final: 0.7521 (t80) REVERT: C 90 GLN cc_start: 0.8544 (mp10) cc_final: 0.8107 (mp10) REVERT: C 176 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8488 (p) REVERT: C 434 MET cc_start: 0.9416 (OUTLIER) cc_final: 0.8756 (mpp) REVERT: D 214 ARG cc_start: 0.9151 (ttp80) cc_final: 0.8775 (mtm110) REVERT: D 445 MET cc_start: 0.9499 (mtm) cc_final: 0.9220 (mtm) REVERT: E 83 MET cc_start: 0.7219 (tpt) cc_final: 0.6742 (tpp) REVERT: E 117 ARG cc_start: 0.9134 (pmm-80) cc_final: 0.8923 (pmm-80) REVERT: E 214 ARG cc_start: 0.9061 (ptt180) cc_final: 0.8800 (ptt180) REVERT: E 445 MET cc_start: 0.9466 (mtm) cc_final: 0.9193 (mtm) REVERT: F 73 ILE cc_start: 0.9055 (tp) cc_final: 0.8821 (pp) REVERT: F 117 ARG cc_start: 0.9178 (ttm-80) cc_final: 0.8934 (ttm-80) REVERT: G 59 MET cc_start: 0.9063 (tpp) cc_final: 0.8845 (tpp) REVERT: G 82 GLN cc_start: 0.8555 (mt0) cc_final: 0.7922 (mt0) REVERT: G 83 MET cc_start: 0.8467 (mmm) cc_final: 0.8217 (tpp) REVERT: G 155 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7972 (pp20) outliers start: 50 outliers final: 22 residues processed: 237 average time/residue: 0.6581 time to fit residues: 174.9760 Evaluate side-chains 218 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 308 ASN Chi-restraints excluded: chain C residue 376 ARG Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 434 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 215 optimal weight: 4.9990 chunk 243 optimal weight: 0.0970 chunk 213 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 125 optimal weight: 8.9990 chunk 33 optimal weight: 0.6980 chunk 176 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 95 optimal weight: 0.3980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 429 GLN B 347 ASN D 429 GLN ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS ** F 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.069003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.046587 restraints weight = 72134.059| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.59 r_work: 0.2686 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22050 Z= 0.109 Angle : 0.583 9.510 29820 Z= 0.283 Chirality : 0.040 0.212 3290 Planarity : 0.004 0.052 3752 Dihedral : 9.361 161.062 3198 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.13 % Favored : 96.83 % Rotamer: Outliers : 1.76 % Allowed : 20.55 % Favored : 77.69 % 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: 1.65 (0.17), residues: 2653 helix: 2.45 (0.16), residues: 1197 sheet: -0.04 (0.21), residues: 637 loop : 0.09 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 117 TYR 0.021 0.001 TYR A 80 PHE 0.008 0.001 PHE A 99 TRP 0.021 0.001 TRP B 142 HIS 0.003 0.000 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (22043) covalent geometry : angle 0.58313 / 0.28 (29820) hydrogen bonds : bond 0.02755 / 1.83 ( 1106) hydrogen bonds : angle 4.13265 / 3.00 ( 3060) Misc. bond : bond 0.00164 / 0.11 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 204 time to evaluate : 0.874 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: A 59 MET cc_start: 0.9124 (tpt) cc_final: 0.8893 (tpp) REVERT: A 82 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7895 (mp10) REVERT: A 108 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7254 (tp-100) REVERT: A 117 ARG cc_start: 0.9085 (ttm-80) cc_final: 0.8748 (ttm-80) REVERT: A 214 ARG cc_start: 0.9096 (ptt180) cc_final: 0.8772 (ptt180) REVERT: B 83 MET cc_start: 0.8182 (mmm) cc_final: 0.7865 (mmm) REVERT: C 87 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7790 (pp) REVERT: C 90 GLN cc_start: 0.8466 (mp10) cc_final: 0.8014 (mp10) REVERT: C 176 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8488 (p) REVERT: C 434 MET cc_start: 0.9377 (OUTLIER) cc_final: 0.8704 (mpp) REVERT: D 214 ARG cc_start: 0.9118 (ttp80) cc_final: 0.8756 (mtm110) REVERT: D 445 MET cc_start: 0.9462 (mtm) cc_final: 0.9172 (mtm) REVERT: E 82 GLN cc_start: 0.8674 (mt0) cc_final: 0.7986 (mt0) REVERT: E 83 MET cc_start: 0.7151 (tpt) cc_final: 0.6683 (tpp) REVERT: E 117 ARG cc_start: 0.9181 (OUTLIER) cc_final: 0.8939 (pmm-80) REVERT: E 399 MET cc_start: 0.9417 (mmm) cc_final: 0.9212 (mmm) REVERT: E 445 MET cc_start: 0.9424 (mtm) cc_final: 0.9151 (mtm) REVERT: F 73 ILE cc_start: 0.9052 (tp) cc_final: 0.8814 (pp) REVERT: F 117 ARG cc_start: 0.9182 (ttm-80) cc_final: 0.8941 (ttm-80) REVERT: G 59 MET cc_start: 0.9066 (tpp) cc_final: 0.8857 (tpp) REVERT: G 82 GLN cc_start: 0.8564 (mt0) cc_final: 0.7915 (mt0) REVERT: G 83 MET cc_start: 0.8439 (mmm) cc_final: 0.8155 (tpp) REVERT: G 155 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7941 (pp20) outliers start: 41 outliers final: 17 residues processed: 241 average time/residue: 0.6696 time to fit residues: 180.3601 Evaluate side-chains 221 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 199 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 308 ASN Chi-restraints excluded: chain C residue 376 ARG Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 117 ARG Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain G residue 86 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 53 optimal weight: 5.9990 chunk 230 optimal weight: 30.0000 chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 198 optimal weight: 9.9990 chunk 241 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.067541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.044682 restraints weight = 72836.511| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 3.64 r_work: 0.2632 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22050 Z= 0.195 Angle : 0.629 9.725 29820 Z= 0.307 Chirality : 0.042 0.216 3290 Planarity : 0.004 0.072 3752 Dihedral : 9.300 175.090 3198 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.32 % Favored : 96.65 % Rotamer: Outliers : 1.93 % Allowed : 21.11 % Favored : 76.96 % 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: 1.71 (0.17), residues: 2653 helix: 2.50 (0.16), residues: 1197 sheet: -0.06 (0.20), residues: 658 loop : 0.17 (0.24), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 117 TYR 0.022 0.001 TYR G 80 PHE 0.015 0.001 PHE B 276 TRP 0.024 0.001 TRP B 142 HIS 0.002 0.001 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (22043) covalent geometry : angle 0.62890 / 0.31 (29820) hydrogen bonds : bond 0.03058 / 2.03 ( 1106) hydrogen bonds : angle 4.15542 / 3.02 ( 3060) Misc. bond : bond 0.00234 / 0.15 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 194 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 MET cc_start: 0.9129 (tpt) cc_final: 0.8888 (tpp) REVERT: A 82 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7858 (mp10) REVERT: A 108 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7279 (tp-100) REVERT: A 146 LYS cc_start: 0.9426 (OUTLIER) cc_final: 0.9056 (mttp) REVERT: A 246 MET cc_start: 0.9488 (mtp) cc_final: 0.9279 (mtp) REVERT: B 83 MET cc_start: 0.8254 (mmm) cc_final: 0.7912 (mmm) REVERT: B 90 GLN cc_start: 0.8631 (mp10) cc_final: 0.8281 (mp-120) REVERT: C 51 TYR cc_start: 0.7920 (t80) cc_final: 0.7478 (t80) REVERT: C 90 GLN cc_start: 0.8439 (mp10) cc_final: 0.8024 (mp10) REVERT: C 176 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8430 (p) REVERT: C 434 MET cc_start: 0.9408 (OUTLIER) cc_final: 0.8741 (mpp) REVERT: C 445 MET cc_start: 0.9212 (mtp) cc_final: 0.8889 (mtm) REVERT: D 214 ARG cc_start: 0.9163 (ttp80) cc_final: 0.8947 (mtm110) REVERT: D 445 MET cc_start: 0.9504 (mtm) cc_final: 0.9218 (mtm) REVERT: E 82 GLN cc_start: 0.8670 (mt0) cc_final: 0.8165 (mt0) REVERT: E 83 MET cc_start: 0.7239 (tpt) cc_final: 0.6755 (tpp) REVERT: E 117 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8930 (pmm-80) REVERT: E 214 ARG cc_start: 0.9091 (ptt180) cc_final: 0.8839 (ptt180) REVERT: E 445 MET cc_start: 0.9458 (mtm) cc_final: 0.9197 (mtm) REVERT: F 73 ILE cc_start: 0.9044 (tp) cc_final: 0.8822 (pp) REVERT: F 117 ARG cc_start: 0.9179 (ttm-80) cc_final: 0.8943 (ttm-80) REVERT: G 59 MET cc_start: 0.9066 (tpp) cc_final: 0.8854 (tpp) REVERT: G 82 GLN cc_start: 0.8521 (mt0) cc_final: 0.8111 (mt0) REVERT: G 83 MET cc_start: 0.8462 (mmm) cc_final: 0.8183 (tpp) REVERT: G 155 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7979 (pp20) outliers start: 45 outliers final: 18 residues processed: 232 average time/residue: 0.6796 time to fit residues: 176.8867 Evaluate side-chains 217 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 376 ARG Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 117 ARG Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 241 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 139 optimal weight: 0.9980 chunk 38 optimal weight: 0.0050 chunk 166 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 197 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 224 optimal weight: 1.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.069229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.046466 restraints weight = 72514.401| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 3.68 r_work: 0.2687 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22050 Z= 0.110 Angle : 0.611 10.969 29820 Z= 0.294 Chirality : 0.041 0.246 3290 Planarity : 0.004 0.051 3752 Dihedral : 8.788 161.794 3194 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.24 % Favored : 96.72 % Rotamer: Outliers : 1.54 % Allowed : 21.62 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.17), residues: 2653 helix: 2.49 (0.16), residues: 1197 sheet: -0.04 (0.20), residues: 644 loop : 0.23 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 156 TYR 0.025 0.001 TYR E 178 PHE 0.008 0.001 PHE B 412 TRP 0.021 0.001 TRP B 142 HIS 0.006 0.001 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (22043) covalent geometry : angle 0.61129 / 0.29 (29820) hydrogen bonds : bond 0.02681 / 1.78 ( 1106) hydrogen bonds : angle 4.09947 / 2.97 ( 3060) Misc. bond : bond 0.00161 / 0.11 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 202 time to evaluate : 0.846 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 82 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7990 (mp10) REVERT: A 108 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7195 (tp-100) REVERT: A 146 LYS cc_start: 0.9411 (OUTLIER) cc_final: 0.9060 (mttp) REVERT: A 246 MET cc_start: 0.9480 (mtp) cc_final: 0.9272 (mtp) REVERT: B 83 MET cc_start: 0.8151 (mmm) cc_final: 0.7795 (mmm) REVERT: B 90 GLN cc_start: 0.8673 (mp10) cc_final: 0.8310 (mp-120) REVERT: C 51 TYR cc_start: 0.7883 (t80) cc_final: 0.7362 (t80) REVERT: C 87 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7790 (pp) REVERT: C 90 GLN cc_start: 0.8356 (mp10) cc_final: 0.7994 (mp10) REVERT: C 176 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8465 (p) REVERT: C 434 MET cc_start: 0.9367 (OUTLIER) cc_final: 0.8696 (mpp) REVERT: C 445 MET cc_start: 0.9199 (mtp) cc_final: 0.8877 (mtm) REVERT: D 445 MET cc_start: 0.9482 (mtm) cc_final: 0.9216 (mtm) REVERT: E 83 MET cc_start: 0.7173 (tpt) cc_final: 0.6662 (tpp) REVERT: E 90 GLN cc_start: 0.7868 (pm20) cc_final: 0.7565 (pm20) REVERT: E 117 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8941 (pmm-80) REVERT: E 214 ARG cc_start: 0.9100 (ptt180) cc_final: 0.8861 (ptt180) REVERT: E 295 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8125 (tm-30) REVERT: E 445 MET cc_start: 0.9433 (mtm) cc_final: 0.9197 (mtm) REVERT: F 73 ILE cc_start: 0.9054 (tp) cc_final: 0.8834 (pp) REVERT: F 117 ARG cc_start: 0.9201 (ttm-80) cc_final: 0.8976 (ttm-80) REVERT: G 59 MET cc_start: 0.9048 (tpp) cc_final: 0.8846 (tpp) REVERT: G 83 MET cc_start: 0.8437 (mmm) cc_final: 0.8160 (tpp) REVERT: G 155 GLU cc_start: 0.8285 (tm-30) cc_final: 0.8034 (pp20) outliers start: 36 outliers final: 17 residues processed: 234 average time/residue: 0.7006 time to fit residues: 183.4713 Evaluate side-chains 219 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 195 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 376 ARG Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 117 ARG Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 295 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 206 optimal weight: 6.9990 chunk 220 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 216 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 435 ASN ** G 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.069204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.046415 restraints weight = 72124.961| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 3.68 r_work: 0.2687 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22050 Z= 0.119 Angle : 0.631 11.753 29820 Z= 0.303 Chirality : 0.041 0.342 3290 Planarity : 0.004 0.049 3752 Dihedral : 8.655 160.469 3194 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.17 % Favored : 96.80 % Rotamer: Outliers : 1.29 % Allowed : 22.48 % Favored : 76.23 % 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: 1.76 (0.17), residues: 2653 helix: 2.50 (0.16), residues: 1197 sheet: -0.05 (0.21), residues: 644 loop : 0.29 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 156 TYR 0.024 0.001 TYR G 80 PHE 0.008 0.001 PHE A 99 TRP 0.018 0.001 TRP B 142 HIS 0.005 0.001 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (22043) covalent geometry : angle 0.63093 / 0.30 (29820) hydrogen bonds : bond 0.02738 / 1.81 ( 1106) hydrogen bonds : angle 4.09221 / 2.97 ( 3060) Misc. bond : bond 0.00164 / 0.11 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 0.782 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: A 108 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7209 (tp-100) REVERT: A 146 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.9067 (mttp) REVERT: A 246 MET cc_start: 0.9488 (mtp) cc_final: 0.9282 (mtp) REVERT: B 83 MET cc_start: 0.8137 (mmm) cc_final: 0.7770 (mmm) REVERT: B 90 GLN cc_start: 0.8659 (mp10) cc_final: 0.8299 (mp-120) REVERT: C 51 TYR cc_start: 0.7906 (t80) cc_final: 0.7386 (t80) REVERT: C 87 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7820 (pp) REVERT: C 90 GLN cc_start: 0.8296 (mp10) cc_final: 0.7908 (mp10) REVERT: C 176 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8438 (p) REVERT: C 445 MET cc_start: 0.9207 (mtp) cc_final: 0.8882 (mtm) REVERT: D 82 GLN cc_start: 0.8223 (tt0) cc_final: 0.7882 (mt0) REVERT: D 214 ARG cc_start: 0.9145 (ttp80) cc_final: 0.8772 (mtm110) REVERT: D 445 MET cc_start: 0.9474 (mtm) cc_final: 0.9209 (mtm) REVERT: E 83 MET cc_start: 0.7161 (tpt) cc_final: 0.6659 (tpp) REVERT: E 117 ARG cc_start: 0.9174 (OUTLIER) cc_final: 0.8939 (pmm-80) REVERT: E 295 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8127 (tm-30) REVERT: E 445 MET cc_start: 0.9438 (mtm) cc_final: 0.9192 (mtm) REVERT: F 73 ILE cc_start: 0.9049 (tp) cc_final: 0.8831 (pp) REVERT: F 117 ARG cc_start: 0.9189 (ttm-80) cc_final: 0.8964 (ttm-80) REVERT: G 59 MET cc_start: 0.9040 (tpp) cc_final: 0.8833 (tpp) REVERT: G 83 MET cc_start: 0.8454 (mmm) cc_final: 0.8174 (tpp) REVERT: G 155 GLU cc_start: 0.8263 (tm-30) cc_final: 0.8026 (pp20) outliers start: 30 outliers final: 19 residues processed: 223 average time/residue: 0.6711 time to fit residues: 166.9261 Evaluate side-chains 216 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 376 ARG Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 117 ARG Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain F residue 58 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 6 optimal weight: 0.0030 chunk 136 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 252 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 139 optimal weight: 0.0030 chunk 134 optimal weight: 0.9990 overall best weight: 0.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.070029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.047326 restraints weight = 72053.041| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.67 r_work: 0.2714 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 22050 Z= 0.107 Angle : 0.640 12.435 29820 Z= 0.304 Chirality : 0.041 0.333 3290 Planarity : 0.004 0.043 3752 Dihedral : 8.248 151.044 3194 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.13 % Favored : 96.83 % Rotamer: Outliers : 0.99 % Allowed : 22.87 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.17), residues: 2653 helix: 2.49 (0.16), residues: 1197 sheet: -0.04 (0.21), residues: 644 loop : 0.34 (0.24), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 156 TYR 0.026 0.001 TYR E 178 PHE 0.011 0.001 PHE B 209 TRP 0.019 0.001 TRP C 251 HIS 0.004 0.000 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (22043) covalent geometry : angle 0.63973 / 0.30 (29820) hydrogen bonds : bond 0.02592 / 1.71 ( 1106) hydrogen bonds : angle 4.08583 / 2.96 ( 3060) Misc. bond : bond 0.00141 / 0.09 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 0.767 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: A 108 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7188 (tp-100) REVERT: A 146 LYS cc_start: 0.9392 (OUTLIER) cc_final: 0.9098 (mttp) REVERT: B 83 MET cc_start: 0.8107 (mmm) cc_final: 0.7733 (mmm) REVERT: B 90 GLN cc_start: 0.8626 (mp10) cc_final: 0.8274 (mp-120) REVERT: C 51 TYR cc_start: 0.7862 (t80) cc_final: 0.7399 (t80) REVERT: C 87 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7840 (pp) REVERT: C 90 GLN cc_start: 0.8266 (mp10) cc_final: 0.7923 (mp10) REVERT: C 176 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8417 (p) REVERT: C 295 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8135 (tm-30) REVERT: D 82 GLN cc_start: 0.8227 (tt0) cc_final: 0.7947 (mt0) REVERT: D 445 MET cc_start: 0.9454 (mtm) cc_final: 0.9198 (mtm) REVERT: E 82 GLN cc_start: 0.8655 (mt0) cc_final: 0.8142 (mt0) REVERT: E 83 MET cc_start: 0.7138 (tpt) cc_final: 0.6652 (tpp) REVERT: E 117 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.8931 (pmm-80) REVERT: E 214 ARG cc_start: 0.9102 (ptt180) cc_final: 0.8857 (ptt-90) REVERT: E 295 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8168 (tm-30) REVERT: E 445 MET cc_start: 0.9450 (mtm) cc_final: 0.9220 (mtm) REVERT: F 73 ILE cc_start: 0.9046 (tp) cc_final: 0.8830 (pp) REVERT: G 83 MET cc_start: 0.8436 (mmm) cc_final: 0.8112 (tpp) REVERT: G 155 GLU cc_start: 0.8273 (tm-30) cc_final: 0.8057 (pp20) outliers start: 23 outliers final: 17 residues processed: 218 average time/residue: 0.7377 time to fit residues: 179.2170 Evaluate side-chains 216 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 376 ARG Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 117 ARG Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain F residue 58 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 169 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 246 optimal weight: 3.9990 chunk 228 optimal weight: 5.9990 chunk 235 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.068593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.046351 restraints weight = 72026.674| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 3.57 r_work: 0.2673 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22050 Z= 0.154 Angle : 0.648 12.406 29820 Z= 0.310 Chirality : 0.041 0.316 3290 Planarity : 0.004 0.058 3752 Dihedral : 8.310 156.640 3194 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.09 % Favored : 96.87 % Rotamer: Outliers : 1.12 % Allowed : 22.69 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.18), residues: 2653 helix: 2.58 (0.16), residues: 1197 sheet: -0.03 (0.21), residues: 644 loop : 0.35 (0.24), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 156 TYR 0.023 0.001 TYR G 80 PHE 0.011 0.001 PHE B 276 TRP 0.016 0.001 TRP B 142 HIS 0.003 0.001 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (22043) covalent geometry : angle 0.64794 / 0.31 (29820) hydrogen bonds : bond 0.02855 / 1.89 ( 1106) hydrogen bonds : angle 4.07602 / 2.96 ( 3060) Misc. bond : bond 0.00194 / 0.13 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7586.52 seconds wall clock time: 130 minutes 12.20 seconds (7812.20 seconds total)