Starting phenix.real_space_refine on Fri Sep 19 00:35:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gsn_51552/09_2025/9gsn_51552.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gsn_51552/09_2025/9gsn_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_51552/09_2025/9gsn_51552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gsn_51552/09_2025/9gsn_51552.map" model { file = "/net/cci-nas-00/data/ceres_data/9gsn_51552/09_2025/9gsn_51552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gsn_51552/09_2025/9gsn_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 5.45, per 1000 atoms: 0.25 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: 1.99 Conformation dependent library (CDL) restraints added in 866.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.02 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: 4.56 Time building geometry restraints manager: 2.59 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=" C ARG A 376 " pdb=" N PRO A 377 " ideal model delta sigma weight residual 1.334 1.353 -0.019 8.40e-03 1.42e+04 5.08e+00 bond pdb=" CB ARG F 77 " pdb=" CG ARG F 77 " ideal model delta sigma weight residual 1.520 1.575 -0.055 3.00e-02 1.11e+03 3.33e+00 bond pdb=" CB GLU F 155 " pdb=" CG GLU F 155 " ideal model delta sigma weight residual 1.520 1.570 -0.050 3.00e-02 1.11e+03 2.80e+00 bond pdb=" CB LYS G 153 " pdb=" CG LYS G 153 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.14e+00 bond pdb=" CB GLN D 122 " pdb=" CG GLN D 122 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 2.00e+00 ... (remaining 22038 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 29261 2.45 - 4.89: 465 4.89 - 7.34: 74 7.34 - 9.78: 14 9.78 - 12.23: 6 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=" 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=" CB MET G 224 " pdb=" CG MET G 224 " pdb=" SD MET G 224 " ideal model delta sigma weight residual 112.70 123.67 -10.97 3.00e+00 1.11e-01 1.34e+01 angle pdb=" CA GLN D 122 " pdb=" CB GLN D 122 " pdb=" CG GLN D 122 " ideal model delta sigma weight residual 114.10 121.37 -7.27 2.00e+00 2.50e-01 1.32e+01 ... (remaining 29815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.46: 12778 33.46 - 66.91: 459 66.91 - 100.37: 38 100.37 - 133.83: 2 133.83 - 167.28: 2 Dihedral angle restraints: 13279 sinusoidal: 5495 harmonic: 7784 Sorted by residual: dihedral pdb=" O1A AGS B 501 " pdb=" O3A AGS B 501 " pdb=" PA AGS B 501 " pdb=" PB AGS B 501 " ideal model delta sinusoidal sigma weight residual -67.73 99.55 -167.28 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" O1A AGS C 502 " pdb=" O3A AGS C 502 " pdb=" PA AGS C 502 " pdb=" PB AGS C 502 " ideal model delta sinusoidal sigma weight residual -67.73 97.88 -165.61 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" O1B 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 68.91 -53.62 122.53 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 13276 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2324 0.035 - 0.070: 670 0.070 - 0.105: 202 0.105 - 0.141: 102 0.141 - 0.176: 6 Chirality restraints: 3304 Sorted by residual: chirality pdb=" CG LEU C 177 " pdb=" CB LEU C 177 " pdb=" CD1 LEU C 177 " pdb=" CD2 LEU C 177 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 7.72e-01 chirality pdb=" CA ILE G 359 " pdb=" N ILE G 359 " pdb=" C ILE G 359 " pdb=" CB ILE G 359 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA ILE A 257 " pdb=" N ILE A 257 " pdb=" C ILE A 257 " pdb=" CB ILE A 257 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 3301 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: 3.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 21.630 Find NCS groups from input model: 0.530 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:7.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 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 : 0.009 0.893 22050 Z= 0.858 Angle : 0.757 12.227 29820 Z= 0.373 Chirality : 0.041 0.176 3304 Planarity : 0.007 0.190 3752 Dihedral : 16.577 167.284 8281 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 aren 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 covalent geometry : bond 0.00372 (22043) covalent geometry : angle 0.75666 (29820) hydrogen bonds : bond 0.17402 ( 1106) hydrogen bonds : angle 6.17095 ( 3060) Misc. bond : bond 0.47309 ( 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 : 0.821 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: 0.7342 time to fit residues: 182.8414 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 : 0.862 ------------------------------------------------------------------------------- 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: 9.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 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 = 0.3445 r_free = 0.3445 target = 0.068710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.046404 restraints weight = 71836.553| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 3.60 r_work: 0.2678 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22050 Z= 0.145 Angle : 0.618 9.675 29820 Z= 0.311 Chirality : 0.043 0.174 3304 Planarity : 0.005 0.091 3752 Dihedral : 9.984 167.388 3086 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.43 % Favored : 96.53 % Rotamer: Outliers : 2.06 % Allowed : 17.63 % Favored : 80.31 % 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 aren not related in a simple way. whole: 1.19 (0.17), residues: 2653 helix: 2.18 (0.16), residues: 1239 sheet: -0.34 (0.21), residues: 595 loop : -0.43 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 117 TYR 0.016 0.001 TYR B 80 PHE 0.015 0.001 PHE G 52 TRP 0.018 0.001 TRP C 251 HIS 0.006 0.001 HIS D 123 Details of bonding type rmsd covalent geometry : bond 0.00331 (22043) covalent geometry : angle 0.61782 (29820) hydrogen bonds : bond 0.04147 ( 1106) hydrogen bonds : angle 4.81014 ( 3060) Misc. bond : bond 0.00189 ( 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 254 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 206 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8354 (mm-40) REVERT: A 108 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7392 (tp-100) REVERT: A 214 ARG cc_start: 0.9077 (ptt180) cc_final: 0.8771 (ptt180) REVERT: B 142 TRP cc_start: 0.8308 (m100) cc_final: 0.8075 (m100) REVERT: C 51 TYR cc_start: 0.7918 (t80) cc_final: 0.7653 (t80) REVERT: C 90 GLN cc_start: 0.8501 (mp10) cc_final: 0.8254 (mp10) REVERT: C 209 PHE cc_start: 0.9164 (t80) cc_final: 0.8680 (t80) REVERT: C 214 ARG cc_start: 0.9143 (mtm110) cc_final: 0.8783 (mtm180) REVERT: D 419 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9213 (tm) REVERT: D 445 MET cc_start: 0.9479 (mtm) cc_final: 0.9204 (mtm) REVERT: E 82 GLN cc_start: 0.8667 (mt0) cc_final: 0.8001 (mt0) REVERT: E 83 MET cc_start: 0.7156 (tpt) cc_final: 0.6647 (tpp) REVERT: E 117 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.8948 (pmm-80) REVERT: E 399 MET cc_start: 0.9476 (mmm) cc_final: 0.9269 (mmm) REVERT: E 445 MET cc_start: 0.9415 (mtm) cc_final: 0.9110 (mtm) REVERT: F 77 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8252 (tpm170) REVERT: F 117 ARG cc_start: 0.9097 (ttm-80) cc_final: 0.8864 (ttm-80) REVERT: F 376 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7048 (ttm-80) REVERT: G 82 GLN cc_start: 0.8615 (mt0) cc_final: 0.8230 (mt0) REVERT: G 83 MET cc_start: 0.8518 (mmm) cc_final: 0.8284 (tpp) REVERT: G 108 GLN cc_start: 0.7478 (tp-100) cc_final: 0.6878 (tt0) outliers start: 48 outliers final: 13 residues processed: 245 average time/residue: 0.7790 time to fit residues: 212.7475 Evaluate side-chains 208 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 190 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 177 LEU Chi-restraints excluded: chain A residue 384 VAL 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 117 ARG Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 376 ARG Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 303 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 0.0970 chunk 245 optimal weight: 0.0570 chunk 261 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 14 optimal weight: 0.2980 chunk 219 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 125 optimal weight: 20.0000 chunk 200 optimal weight: 8.9990 chunk 228 optimal weight: 0.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 = 0.3455 r_free = 0.3455 target = 0.069050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.047087 restraints weight = 71515.629| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.51 r_work: 0.2696 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22050 Z= 0.113 Angle : 0.581 8.781 29820 Z= 0.289 Chirality : 0.041 0.161 3304 Planarity : 0.005 0.082 3752 Dihedral : 9.794 168.510 3075 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.35 % Favored : 96.61 % Rotamer: Outliers : 1.93 % Allowed : 18.32 % Favored : 79.75 % 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 aren not related in a simple way. whole: 1.36 (0.17), residues: 2653 helix: 2.31 (0.16), residues: 1197 sheet: -0.16 (0.21), residues: 595 loop : -0.26 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 156 TYR 0.017 0.001 TYR B 80 PHE 0.008 0.001 PHE B 169 TRP 0.019 0.001 TRP C 251 HIS 0.006 0.001 HIS E 123 Details of bonding type rmsd covalent geometry : bond 0.00250 (22043) covalent geometry : angle 0.58122 (29820) hydrogen bonds : bond 0.03363 ( 1106) hydrogen bonds : angle 4.51658 ( 3060) Misc. bond : bond 0.00235 ( 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 246 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 201 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8251 (mm110) REVERT: A 108 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7274 (tp-100) REVERT: A 445 MET cc_start: 0.9197 (ptm) cc_final: 0.8955 (ptt) REVERT: B 90 GLN cc_start: 0.8273 (mp10) cc_final: 0.8042 (mp10) REVERT: B 425 THR cc_start: 0.9327 (OUTLIER) cc_final: 0.9110 (p) REVERT: C 90 GLN cc_start: 0.8502 (mp10) cc_final: 0.8176 (mp10) REVERT: C 176 THR cc_start: 0.9114 (OUTLIER) cc_final: 0.8749 (p) REVERT: C 445 MET cc_start: 0.9191 (mtp) cc_final: 0.8987 (mtp) REVERT: D 445 MET cc_start: 0.9443 (mtm) cc_final: 0.9167 (mtm) REVERT: E 82 GLN cc_start: 0.8652 (mt0) cc_final: 0.7977 (mt0) REVERT: E 83 MET cc_start: 0.7153 (tpt) cc_final: 0.6677 (tpp) REVERT: E 214 ARG cc_start: 0.9036 (ptt180) cc_final: 0.8764 (ptt180) REVERT: E 445 MET cc_start: 0.9419 (mtm) cc_final: 0.9103 (mtm) REVERT: F 83 MET cc_start: 0.5683 (OUTLIER) cc_final: 0.4947 (mmm) REVERT: F 117 ARG cc_start: 0.9134 (ttm-80) cc_final: 0.8894 (ttm-80) REVERT: F 376 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7032 (ttm-80) REVERT: G 82 GLN cc_start: 0.8615 (mt0) cc_final: 0.8028 (mt0) REVERT: G 83 MET cc_start: 0.8508 (mmm) cc_final: 0.8266 (tpp) REVERT: G 117 ARG cc_start: 0.9213 (tpp80) cc_final: 0.8842 (tpp80) outliers start: 45 outliers final: 9 residues processed: 236 average time/residue: 0.8127 time to fit residues: 213.2888 Evaluate side-chains 205 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 191 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 176 THR Chi-restraints excluded: chain A residue 177 LEU 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 D residue 199 THR Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 376 ARG Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 257 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 242 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 175 optimal weight: 4.9990 chunk 240 optimal weight: 10.0000 chunk 209 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.066940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.044314 restraints weight = 73155.285| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 3.61 r_work: 0.2621 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 22050 Z= 0.238 Angle : 0.605 8.033 29820 Z= 0.303 Chirality : 0.042 0.160 3304 Planarity : 0.005 0.098 3752 Dihedral : 9.809 167.878 3073 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.47 % Favored : 96.49 % Rotamer: Outliers : 1.93 % Allowed : 19.52 % Favored : 78.55 % 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 aren not related in a simple way. whole: 1.43 (0.17), residues: 2653 helix: 2.34 (0.16), residues: 1197 sheet: -0.07 (0.21), residues: 595 loop : -0.22 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 376 TYR 0.018 0.001 TYR A 80 PHE 0.017 0.002 PHE B 276 TRP 0.015 0.001 TRP C 251 HIS 0.005 0.001 HIS F 440 Details of bonding type rmsd covalent geometry : bond 0.00546 (22043) covalent geometry : angle 0.60485 (29820) hydrogen bonds : bond 0.03525 ( 1106) hydrogen bonds : angle 4.42239 ( 3060) Misc. bond : bond 0.00532 ( 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 236 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 191 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8311 (mm110) REVERT: A 108 GLN cc_start: 0.8037 (mm-40) cc_final: 0.7739 (tp-100) REVERT: B 90 GLN cc_start: 0.8041 (mp10) cc_final: 0.7734 (mp10) REVERT: B 214 ARG cc_start: 0.9114 (ttp80) cc_final: 0.8857 (ttp80) REVERT: B 425 THR cc_start: 0.9405 (OUTLIER) cc_final: 0.9186 (p) REVERT: C 51 TYR cc_start: 0.7901 (t80) cc_final: 0.7551 (t80) REVERT: C 90 GLN cc_start: 0.8562 (mp10) cc_final: 0.8122 (mp10) REVERT: C 176 THR cc_start: 0.9133 (OUTLIER) cc_final: 0.8692 (p) REVERT: D 445 MET cc_start: 0.9499 (mtm) cc_final: 0.9235 (mtm) REVERT: E 82 GLN cc_start: 0.8709 (mt0) cc_final: 0.8047 (mt0) REVERT: E 83 MET cc_start: 0.7238 (tpt) cc_final: 0.6718 (tpp) REVERT: E 117 ARG cc_start: 0.9123 (pmm-80) cc_final: 0.8922 (pmm-80) REVERT: E 445 MET cc_start: 0.9481 (mtm) cc_final: 0.9202 (mtm) REVERT: F 73 ILE cc_start: 0.9076 (tp) cc_final: 0.8825 (pp) REVERT: F 83 MET cc_start: 0.5730 (OUTLIER) cc_final: 0.5363 (tpt) REVERT: F 117 ARG cc_start: 0.9151 (ttm-80) cc_final: 0.8894 (ttm-80) REVERT: F 122 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8496 (tp-100) REVERT: G 82 GLN cc_start: 0.8603 (mt0) cc_final: 0.7991 (mt0) REVERT: G 83 MET cc_start: 0.8494 (mmm) cc_final: 0.8245 (tpp) REVERT: G 117 ARG cc_start: 0.9223 (tpp80) cc_final: 0.8832 (tpp80) outliers start: 45 outliers final: 18 residues processed: 229 average time/residue: 0.7694 time to fit residues: 197.3428 Evaluate side-chains 209 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 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 424 SER Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 375 MET Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain F residue 83 MET 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: 0.0030 chunk 37 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 30.0000 chunk 24 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 187 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 200 optimal weight: 7.9990 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN B 429 GLN C 122 GLN ** D 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 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 = 0.3414 r_free = 0.3414 target = 0.067149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.044551 restraints weight = 72821.994| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 3.62 r_work: 0.2627 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 22050 Z= 0.200 Angle : 0.603 9.612 29820 Z= 0.301 Chirality : 0.041 0.162 3304 Planarity : 0.005 0.084 3752 Dihedral : 9.806 168.104 3073 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.43 % Favored : 96.53 % Rotamer: Outliers : 2.36 % Allowed : 19.43 % Favored : 78.21 % 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 aren not related in a simple way. whole: 1.42 (0.17), residues: 2653 helix: 2.33 (0.16), residues: 1197 sheet: -0.24 (0.21), residues: 630 loop : -0.06 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 117 TYR 0.009 0.001 TYR F 382 PHE 0.014 0.001 PHE B 276 TRP 0.019 0.001 TRP B 142 HIS 0.004 0.001 HIS E 123 Details of bonding type rmsd covalent geometry : bond 0.00460 (22043) covalent geometry : angle 0.60302 (29820) hydrogen bonds : bond 0.03318 ( 1106) hydrogen bonds : angle 4.33285 ( 3060) Misc. bond : bond 0.00240 ( 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 248 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 193 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8256 (mt0) REVERT: A 88 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7921 (tm-30) REVERT: A 108 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7290 (tp-100) REVERT: A 117 ARG cc_start: 0.9084 (ttm-80) cc_final: 0.8768 (ttm-80) REVERT: B 90 GLN cc_start: 0.7983 (mp10) cc_final: 0.7594 (mp10) REVERT: B 425 THR cc_start: 0.9406 (OUTLIER) cc_final: 0.9185 (p) REVERT: C 51 TYR cc_start: 0.7903 (t80) cc_final: 0.7482 (t80) REVERT: C 90 GLN cc_start: 0.8570 (mp10) cc_final: 0.8146 (mp10) REVERT: D 87 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7821 (pt) REVERT: D 359 ILE cc_start: 0.9728 (OUTLIER) cc_final: 0.9444 (mm) REVERT: D 445 MET cc_start: 0.9494 (mtm) cc_final: 0.9196 (mtm) REVERT: E 82 GLN cc_start: 0.8711 (mt0) cc_final: 0.8039 (mt0) REVERT: E 83 MET cc_start: 0.7157 (tpt) cc_final: 0.6645 (tpp) REVERT: E 117 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8911 (pmm-80) REVERT: E 445 MET cc_start: 0.9483 (mtm) cc_final: 0.9199 (mtm) REVERT: F 73 ILE cc_start: 0.9045 (tp) cc_final: 0.8802 (pp) REVERT: F 83 MET cc_start: 0.5638 (OUTLIER) cc_final: 0.5220 (tpt) REVERT: F 90 GLN cc_start: 0.7685 (pm20) cc_final: 0.7479 (pm20) REVERT: F 117 ARG cc_start: 0.9182 (ttm-80) cc_final: 0.8936 (ttm-80) REVERT: G 82 GLN cc_start: 0.8569 (mt0) cc_final: 0.8199 (mt0) REVERT: G 83 MET cc_start: 0.8479 (mmm) cc_final: 0.8223 (tpp) outliers start: 55 outliers final: 24 residues processed: 237 average time/residue: 0.7390 time to fit residues: 196.3201 Evaluate side-chains 215 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 176 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 123 HIS 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 308 ASN Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 359 ILE 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 E residue 425 THR Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 397 MET Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 375 MET 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: 0.0060 chunk 243 optimal weight: 0.4980 chunk 213 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 143 optimal weight: 8.9990 chunk 175 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN ** C 122 GLN ** 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 = 0.3447 r_free = 0.3447 target = 0.068715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.046149 restraints weight = 71933.533| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 3.64 r_work: 0.2681 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 22050 Z= 0.108 Angle : 0.593 10.777 29820 Z= 0.292 Chirality : 0.040 0.162 3304 Planarity : 0.004 0.063 3752 Dihedral : 9.711 167.783 3070 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.17 % Favored : 96.80 % Rotamer: Outliers : 2.02 % Allowed : 20.46 % Favored : 77.52 % 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 aren not related in a simple way. whole: 1.45 (0.17), residues: 2653 helix: 2.33 (0.16), residues: 1197 sheet: -0.14 (0.21), residues: 637 loop : -0.09 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 117 TYR 0.021 0.001 TYR A 80 PHE 0.007 0.001 PHE G 401 TRP 0.024 0.001 TRP B 142 HIS 0.004 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00245 (22043) covalent geometry : angle 0.59267 (29820) hydrogen bonds : bond 0.02952 ( 1106) hydrogen bonds : angle 4.27098 ( 3060) Misc. bond : bond 0.00148 ( 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 247 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 200 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7230 (tp-100) REVERT: A 117 ARG cc_start: 0.9084 (ttm-80) cc_final: 0.8783 (ttm-80) REVERT: B 90 GLN cc_start: 0.7951 (mp10) cc_final: 0.7423 (mp10) REVERT: B 425 THR cc_start: 0.9349 (OUTLIER) cc_final: 0.9142 (p) REVERT: C 51 TYR cc_start: 0.7886 (t80) cc_final: 0.7484 (t80) REVERT: C 90 GLN cc_start: 0.8529 (mp10) cc_final: 0.8079 (mp10) REVERT: D 445 MET cc_start: 0.9416 (mtm) cc_final: 0.9075 (mtm) REVERT: E 82 GLN cc_start: 0.8682 (mt0) cc_final: 0.7973 (mt0) REVERT: E 83 MET cc_start: 0.7093 (tpt) cc_final: 0.6619 (tpp) REVERT: E 117 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.8924 (pmm-80) REVERT: E 445 MET cc_start: 0.9404 (mtm) cc_final: 0.9087 (mtm) REVERT: F 73 ILE cc_start: 0.9050 (tp) cc_final: 0.8805 (pp) REVERT: F 117 ARG cc_start: 0.9186 (ttm-80) cc_final: 0.8938 (ttm-80) REVERT: G 83 MET cc_start: 0.8471 (mmm) cc_final: 0.8195 (tpp) REVERT: G 425 THR cc_start: 0.9298 (OUTLIER) cc_final: 0.9087 (p) outliers start: 47 outliers final: 20 residues processed: 237 average time/residue: 0.7449 time to fit residues: 197.3857 Evaluate side-chains 214 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 191 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 A residue 434 MET Chi-restraints excluded: chain B residue 123 HIS 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 308 ASN Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 375 MET 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 F residue 72 ILE Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 425 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 53 optimal weight: 1.9990 chunk 230 optimal weight: 9.9990 chunk 43 optimal weight: 0.5980 chunk 67 optimal weight: 7.9990 chunk 150 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 241 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 ASN F 106 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.068338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.045596 restraints weight = 72379.911| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 3.66 r_work: 0.2661 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22050 Z= 0.137 Angle : 0.607 9.788 29820 Z= 0.296 Chirality : 0.041 0.201 3304 Planarity : 0.004 0.062 3752 Dihedral : 9.656 166.840 3070 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.28 % Favored : 96.68 % Rotamer: Outliers : 2.02 % Allowed : 21.15 % 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 aren not related in a simple way. whole: 1.54 (0.17), residues: 2653 helix: 2.40 (0.16), residues: 1197 sheet: -0.11 (0.21), residues: 637 loop : -0.03 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 214 TYR 0.026 0.001 TYR E 178 PHE 0.009 0.001 PHE B 276 TRP 0.026 0.001 TRP B 142 HIS 0.004 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00320 (22043) covalent geometry : angle 0.60671 (29820) hydrogen bonds : bond 0.02939 ( 1106) hydrogen bonds : angle 4.21540 ( 3060) Misc. bond : bond 0.00164 ( 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 238 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 191 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7603 (tp-100) REVERT: A 117 ARG cc_start: 0.9088 (ttm-80) cc_final: 0.8768 (ttm-80) REVERT: B 90 GLN cc_start: 0.7902 (mp10) cc_final: 0.7351 (mp10) REVERT: B 425 THR cc_start: 0.9352 (OUTLIER) cc_final: 0.9142 (p) REVERT: C 51 TYR cc_start: 0.7915 (t80) cc_final: 0.7528 (t80) REVERT: C 90 GLN cc_start: 0.8490 (mp10) cc_final: 0.8066 (mp10) REVERT: D 87 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7764 (pt) REVERT: D 445 MET cc_start: 0.9431 (mtm) cc_final: 0.9112 (mtm) REVERT: E 82 GLN cc_start: 0.8679 (mt0) cc_final: 0.7975 (mt0) REVERT: E 83 MET cc_start: 0.7127 (tpt) cc_final: 0.6651 (tpp) REVERT: E 117 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8930 (pmm-80) REVERT: E 445 MET cc_start: 0.9428 (mtm) cc_final: 0.9126 (mtm) REVERT: F 73 ILE cc_start: 0.9051 (tp) cc_final: 0.8809 (pp) REVERT: F 117 ARG cc_start: 0.9183 (ttm-80) cc_final: 0.8935 (ttm-80) REVERT: G 83 MET cc_start: 0.8473 (mmm) cc_final: 0.8196 (tpp) REVERT: G 425 THR cc_start: 0.9308 (OUTLIER) cc_final: 0.9090 (p) outliers start: 47 outliers final: 24 residues processed: 231 average time/residue: 0.6425 time to fit residues: 166.3406 Evaluate side-chains 215 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 194 ILE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 123 HIS 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 308 ASN Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 275 SER 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 F residue 85 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 375 MET Chi-restraints excluded: chain G residue 425 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 241 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 139 optimal weight: 0.9980 chunk 38 optimal weight: 20.0000 chunk 166 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 197 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.067900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.045100 restraints weight = 72800.350| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 3.66 r_work: 0.2645 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.2016 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= 0.164 Angle : 0.624 10.598 29820 Z= 0.306 Chirality : 0.041 0.197 3304 Planarity : 0.004 0.067 3752 Dihedral : 9.663 167.045 3070 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.24 % Favored : 96.72 % Rotamer: Outliers : 1.97 % Allowed : 21.45 % Favored : 76.58 % 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 aren not related in a simple way. whole: 1.57 (0.17), residues: 2653 helix: 2.42 (0.16), residues: 1197 sheet: -0.11 (0.20), residues: 637 loop : 0.00 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 156 TYR 0.023 0.001 TYR G 80 PHE 0.014 0.001 PHE B 209 TRP 0.029 0.001 TRP B 142 HIS 0.005 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00381 (22043) covalent geometry : angle 0.62442 (29820) hydrogen bonds : bond 0.03017 ( 1106) hydrogen bonds : angle 4.19920 ( 3060) Misc. bond : bond 0.00199 ( 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 235 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 189 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.7948 (mm-40) cc_final: 0.7253 (tp-100) REVERT: B 90 GLN cc_start: 0.7861 (mp10) cc_final: 0.7297 (mp10) REVERT: B 209 PHE cc_start: 0.9037 (t80) cc_final: 0.8637 (t80) REVERT: C 51 TYR cc_start: 0.7899 (t80) cc_final: 0.7474 (t80) REVERT: C 90 GLN cc_start: 0.8438 (mp10) cc_final: 0.8020 (mp10) REVERT: C 445 MET cc_start: 0.9227 (mtp) cc_final: 0.8874 (mtm) REVERT: D 87 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7759 (pt) REVERT: D 445 MET cc_start: 0.9459 (mtm) cc_final: 0.9145 (mtm) REVERT: E 82 GLN cc_start: 0.8704 (mt0) cc_final: 0.7982 (mt0) REVERT: E 83 MET cc_start: 0.7152 (tpt) cc_final: 0.6682 (tpp) REVERT: E 117 ARG cc_start: 0.9171 (OUTLIER) cc_final: 0.8941 (pmm-80) REVERT: E 445 MET cc_start: 0.9456 (mtm) cc_final: 0.9169 (mtm) REVERT: F 73 ILE cc_start: 0.9063 (tp) cc_final: 0.8828 (pp) REVERT: F 117 ARG cc_start: 0.9195 (ttm-80) cc_final: 0.8948 (ttm-80) REVERT: G 83 MET cc_start: 0.8466 (mmm) cc_final: 0.8188 (tpp) REVERT: G 425 THR cc_start: 0.9320 (OUTLIER) cc_final: 0.9101 (p) outliers start: 46 outliers final: 23 residues processed: 229 average time/residue: 0.7285 time to fit residues: 186.5545 Evaluate side-chains 213 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 194 ILE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain C residue 308 ASN Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 275 SER 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 F residue 85 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 375 MET Chi-restraints excluded: chain G residue 425 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 206 optimal weight: 8.9990 chunk 220 optimal weight: 0.9980 chunk 214 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 216 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 93 optimal weight: 0.0770 chunk 75 optimal weight: 3.9990 overall best weight: 1.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** E 113 HIS ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.069318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.047022 restraints weight = 71736.726| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 3.62 r_work: 0.2701 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.2109 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= 0.116 Angle : 0.639 11.318 29820 Z= 0.307 Chirality : 0.041 0.268 3304 Planarity : 0.004 0.055 3752 Dihedral : 9.611 164.995 3070 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.39 % Favored : 96.57 % Rotamer: Outliers : 1.33 % Allowed : 22.09 % Favored : 76.58 % 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 aren not related in a simple way. whole: 1.56 (0.17), residues: 2653 helix: 2.39 (0.16), residues: 1197 sheet: -0.11 (0.20), residues: 637 loop : 0.04 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 117 TYR 0.022 0.001 TYR E 178 PHE 0.008 0.001 PHE G 401 TRP 0.023 0.001 TRP B 142 HIS 0.004 0.000 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00271 (22043) covalent geometry : angle 0.63884 (29820) hydrogen bonds : bond 0.02804 ( 1106) hydrogen bonds : angle 4.18189 ( 3060) Misc. bond : bond 0.00150 ( 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 228 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 197 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7867 (mp10) REVERT: A 108 GLN cc_start: 0.7906 (mm-40) cc_final: 0.7221 (tp-100) REVERT: B 90 GLN cc_start: 0.7774 (mp10) cc_final: 0.7535 (mp10) REVERT: C 51 TYR cc_start: 0.7873 (t80) cc_final: 0.7466 (t80) REVERT: C 90 GLN cc_start: 0.8416 (mp10) cc_final: 0.8034 (mp10) REVERT: C 445 MET cc_start: 0.9181 (mtp) cc_final: 0.8830 (mtm) REVERT: D 87 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7738 (pt) REVERT: D 445 MET cc_start: 0.9396 (mtm) cc_final: 0.9061 (mtm) REVERT: E 82 GLN cc_start: 0.8689 (mt0) cc_final: 0.7958 (mt0) REVERT: E 83 MET cc_start: 0.7104 (tpt) cc_final: 0.6627 (tpp) REVERT: E 90 GLN cc_start: 0.7962 (pm20) cc_final: 0.7610 (pm20) REVERT: E 117 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8925 (pmm-80) REVERT: E 445 MET cc_start: 0.9433 (mtm) cc_final: 0.9149 (mtm) REVERT: F 73 ILE cc_start: 0.9040 (tp) cc_final: 0.8807 (pp) REVERT: F 83 MET cc_start: 0.5552 (OUTLIER) cc_final: 0.5156 (tpt) REVERT: F 117 ARG cc_start: 0.9192 (ttm-80) cc_final: 0.8947 (ttm-80) REVERT: G 83 MET cc_start: 0.8455 (mmm) cc_final: 0.8145 (tpp) outliers start: 31 outliers final: 20 residues processed: 222 average time/residue: 0.7319 time to fit residues: 181.0060 Evaluate side-chains 218 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 194 ILE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 308 ASN Chi-restraints excluded: chain D residue 87 LEU 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 F residue 83 MET Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 375 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 6 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 11 optimal weight: 20.0000 chunk 252 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 37 optimal weight: 0.3980 chunk 1 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 139 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** 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 = 0.3460 r_free = 0.3460 target = 0.069338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.047053 restraints weight = 71822.391| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 3.61 r_work: 0.2699 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22050 Z= 0.124 Angle : 0.651 12.182 29820 Z= 0.313 Chirality : 0.041 0.335 3304 Planarity : 0.004 0.056 3752 Dihedral : 9.540 163.807 3070 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.32 % Favored : 96.65 % Rotamer: Outliers : 1.46 % Allowed : 22.39 % 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 aren not related in a simple way. whole: 1.63 (0.17), residues: 2653 helix: 2.43 (0.16), residues: 1197 sheet: -0.06 (0.21), residues: 637 loop : 0.09 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 117 TYR 0.025 0.001 TYR G 80 PHE 0.008 0.001 PHE A 99 TRP 0.022 0.001 TRP B 142 HIS 0.005 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00289 (22043) covalent geometry : angle 0.65066 (29820) hydrogen bonds : bond 0.02826 ( 1106) hydrogen bonds : angle 4.19015 ( 3060) Misc. bond : bond 0.00155 ( 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 229 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.7904 (mm-40) cc_final: 0.7225 (tp-100) REVERT: A 214 ARG cc_start: 0.9133 (ptt180) cc_final: 0.8877 (ptt180) REVERT: C 87 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7784 (pp) REVERT: C 90 GLN cc_start: 0.8374 (mp10) cc_final: 0.7990 (mp10) REVERT: C 445 MET cc_start: 0.9190 (mtp) cc_final: 0.8833 (mtm) REVERT: D 87 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7744 (pt) REVERT: D 214 ARG cc_start: 0.9087 (ttp80) cc_final: 0.8677 (mtm110) REVERT: D 445 MET cc_start: 0.9420 (mtm) cc_final: 0.9103 (mtm) REVERT: E 82 GLN cc_start: 0.8702 (mt0) cc_final: 0.7956 (mt0) REVERT: E 83 MET cc_start: 0.7175 (tpt) cc_final: 0.6667 (tpp) REVERT: E 117 ARG cc_start: 0.9178 (OUTLIER) cc_final: 0.8947 (pmm-80) REVERT: E 445 MET cc_start: 0.9436 (mtm) cc_final: 0.9163 (mtm) REVERT: F 73 ILE cc_start: 0.9057 (tp) cc_final: 0.8830 (pp) REVERT: F 117 ARG cc_start: 0.9209 (ttm-80) cc_final: 0.8974 (ttm-80) REVERT: G 83 MET cc_start: 0.8482 (mmm) cc_final: 0.8175 (tpp) outliers start: 34 outliers final: 26 residues processed: 223 average time/residue: 0.8214 time to fit residues: 203.9281 Evaluate side-chains 221 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 194 ILE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 308 ASN Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 275 SER 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 E residue 397 MET Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 375 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 169 optimal weight: 0.0470 chunk 4 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 246 optimal weight: 2.9990 chunk 228 optimal weight: 0.7980 chunk 235 optimal weight: 9.9990 chunk 30 optimal weight: 0.6980 chunk 154 optimal weight: 8.9990 chunk 175 optimal weight: 2.9990 overall best weight: 1.0680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** 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 = 0.3461 r_free = 0.3461 target = 0.069348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.046622 restraints weight = 72056.723| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 3.67 r_work: 0.2693 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22050 Z= 0.118 Angle : 0.646 12.212 29820 Z= 0.310 Chirality : 0.041 0.297 3304 Planarity : 0.004 0.052 3752 Dihedral : 9.505 163.474 3070 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.32 % Favored : 96.65 % Rotamer: Outliers : 1.37 % Allowed : 22.48 % 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 aren not related in a simple way. whole: 1.64 (0.17), residues: 2653 helix: 2.42 (0.16), residues: 1197 sheet: -0.07 (0.21), residues: 623 loop : 0.13 (0.23), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 117 TYR 0.024 0.001 TYR E 178 PHE 0.007 0.001 PHE A 99 TRP 0.021 0.001 TRP B 142 HIS 0.006 0.001 HIS D 123 Details of bonding type rmsd covalent geometry : bond 0.00277 (22043) covalent geometry : angle 0.64626 (29820) hydrogen bonds : bond 0.02759 ( 1106) hydrogen bonds : angle 4.16707 ( 3060) Misc. bond : bond 0.00143 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8179.46 seconds wall clock time: 140 minutes 9.05 seconds (8409.05 seconds total)