Starting phenix.real_space_refine on Thu Mar 5 15:37:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rwb_24713/03_2026/7rwb_24713.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rwb_24713/03_2026/7rwb_24713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rwb_24713/03_2026/7rwb_24713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rwb_24713/03_2026/7rwb_24713.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rwb_24713/03_2026/7rwb_24713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rwb_24713/03_2026/7rwb_24713.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 15450 2.51 5 N 4140 2.21 5 O 4282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23962 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4662 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 22, 'TRANS': 589} Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 14, 'ASP:plan': 10, 'ARG:plan': 5, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 115 Chain: "B" Number of atoms: 3512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 3512 Classifications: {'peptide': 557} Incomplete info: {'truncation_to_alanine': 282} Link IDs: {'PTRANS': 26, 'TRANS': 530} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 923 Unresolved non-hydrogen angles: 1153 Unresolved non-hydrogen dihedrals: 734 Unresolved non-hydrogen chiralities: 74 Planarities with less than four sites: {'GLU:plan': 38, 'ARG:plan': 12, 'ASP:plan': 30, 'ASN:plan1': 21, 'GLN:plan1': 14, 'TYR:plan': 7, 'PHE:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 498 Chain: "M" Number of atoms: 2692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 2692 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'PTRANS': 17, 'TRANS': 375} Chain breaks: 2 Unresolved non-hydrogen bonds: 492 Unresolved non-hydrogen angles: 592 Unresolved non-hydrogen dihedrals: 411 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLU:plan': 17, 'ARG:plan': 21, 'ASP:plan': 10, 'GLN:plan1': 8, 'ASN:plan1': 8, 'TYR:plan': 2, 'PHE:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 299 Chain: "S" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1115 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 141} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 5, 'GLU:plan': 5, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 60 Restraints were copied for chains: a, b, m, s Time building chain proxies: 6.84, per 1000 atoms: 0.29 Number of scatterers: 23962 At special positions: 0 Unit cell: (132.09, 187.59, 124.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 4282 8.00 N 4140 7.00 C 15450 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 1.0 seconds 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6588 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 14 sheets defined 63.0% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 removed outlier: 3.549A pdb=" N VAL A 15 " --> pdb=" O ARG A 11 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN A 22 " --> pdb=" O SER A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 45 removed outlier: 3.674A pdb=" N GLU A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 69 removed outlier: 3.891A pdb=" N GLY A 69 " --> pdb=" O ILE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 81 Processing helix chain 'A' and resid 87 through 101 Processing helix chain 'A' and resid 105 through 121 Processing helix chain 'A' and resid 124 through 139 removed outlier: 3.969A pdb=" N VAL A 138 " --> pdb=" O CYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 150 through 156 Processing helix chain 'A' and resid 161 through 179 Processing helix chain 'A' and resid 180 through 183 removed outlier: 3.745A pdb=" N VAL A 183 " --> pdb=" O PRO A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 183' Processing helix chain 'A' and resid 188 through 196 removed outlier: 3.862A pdb=" N HIS A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 218 Processing helix chain 'A' and resid 219 through 223 removed outlier: 3.891A pdb=" N LYS A 223 " --> pdb=" O GLU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 removed outlier: 4.008A pdb=" N LEU A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 254 through 267 Processing helix chain 'A' and resid 273 through 293 Processing helix chain 'A' and resid 299 through 321 removed outlier: 4.083A pdb=" N SER A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 Processing helix chain 'A' and resid 342 through 357 removed outlier: 3.936A pdb=" N ARG A 346 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 361 removed outlier: 6.004A pdb=" N PHE A 361 " --> pdb=" O SER A 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 358 through 361' Processing helix chain 'A' and resid 362 through 368 Processing helix chain 'A' and resid 369 through 380 removed outlier: 3.833A pdb=" N GLU A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 396 removed outlier: 3.630A pdb=" N GLN A 387 " --> pdb=" O VAL A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 416 removed outlier: 3.645A pdb=" N ILE A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'A' and resid 420 through 435 Processing helix chain 'A' and resid 438 through 453 removed outlier: 3.801A pdb=" N TYR A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 473 removed outlier: 3.784A pdb=" N ASP A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 488 removed outlier: 3.683A pdb=" N GLN A 488 " --> pdb=" O PHE A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 508 Processing helix chain 'A' and resid 514 through 517 Processing helix chain 'A' and resid 518 through 531 removed outlier: 3.592A pdb=" N HIS A 531 " --> pdb=" O HIS A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 552 removed outlier: 3.914A pdb=" N ASN A 550 " --> pdb=" O ILE A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 564 Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 573 through 590 removed outlier: 3.711A pdb=" N ALA A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 610 through 620 removed outlier: 3.507A pdb=" N ALA A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 44 Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 50 through 58 Processing helix chain 'B' and resid 62 through 78 Processing helix chain 'B' and resid 81 through 86 removed outlier: 3.607A pdb=" N ILE B 85 " --> pdb=" O ASP B 82 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N MET B 86 " --> pdb=" O MET B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 96 Processing helix chain 'B' and resid 99 through 112 removed outlier: 3.862A pdb=" N CYS B 112 " --> pdb=" O ARG B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 removed outlier: 4.567A pdb=" N GLU B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Proline residue: B 125 - end of helix Processing helix chain 'B' and resid 134 through 151 removed outlier: 3.888A pdb=" N ASP B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 170 removed outlier: 4.001A pdb=" N GLN B 159 " --> pdb=" O MET B 155 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA B 170 " --> pdb=" O ARG B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 188 Processing helix chain 'B' and resid 202 through 213 Processing helix chain 'B' and resid 215 through 227 Processing helix chain 'B' and resid 233 through 244 removed outlier: 3.845A pdb=" N ALA B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 266 removed outlier: 3.890A pdb=" N VAL B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 291 Proline residue: B 286 - end of helix Processing helix chain 'B' and resid 295 through 313 Processing helix chain 'B' and resid 320 through 325 Processing helix chain 'B' and resid 331 through 345 Processing helix chain 'B' and resid 350 through 362 Processing helix chain 'B' and resid 366 through 384 Processing helix chain 'B' and resid 387 through 400 removed outlier: 3.544A pdb=" N GLN B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 419 removed outlier: 3.538A pdb=" N ARG B 419 " --> pdb=" O ARG B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 428 through 435 removed outlier: 3.693A pdb=" N LEU B 432 " --> pdb=" O ILE B 428 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASN B 435 " --> pdb=" O THR B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 455 Processing helix chain 'B' and resid 461 through 470 Processing helix chain 'B' and resid 477 through 495 Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 516 through 531 Processing helix chain 'B' and resid 533 through 541 Processing helix chain 'B' and resid 556 through 565 removed outlier: 3.616A pdb=" N CYS B 565 " --> pdb=" O ASP B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 575 removed outlier: 4.176A pdb=" N VAL B 573 " --> pdb=" O SER B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 581 Processing helix chain 'M' and resid 25 through 37 removed outlier: 3.517A pdb=" N VAL M 29 " --> pdb=" O GLY M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 94 removed outlier: 3.522A pdb=" N VAL M 78 " --> pdb=" O ASN M 74 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE M 79 " --> pdb=" O ALA M 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 104 Processing helix chain 'M' and resid 104 through 115 Processing helix chain 'M' and resid 125 through 133 removed outlier: 3.632A pdb=" N THR M 131 " --> pdb=" O GLY M 127 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE M 132 " --> pdb=" O ALA M 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 379 through 383 removed outlier: 3.584A pdb=" N ALA M 382 " --> pdb=" O LYS M 379 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG M 383 " --> pdb=" O LYS M 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 379 through 383' Processing helix chain 'M' and resid 414 through 418 Processing helix chain 'S' and resid 24 through 42 removed outlier: 3.660A pdb=" N LYS S 28 " --> pdb=" O ASP S 24 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN S 29 " --> pdb=" O ASP S 25 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL S 41 " --> pdb=" O ALA S 37 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 96 Processing helix chain 'S' and resid 99 through 106 Processing helix chain 'S' and resid 106 through 118 Processing helix chain 'S' and resid 128 through 138 Processing helix chain 'a' and resid 11 through 22 removed outlier: 3.549A pdb=" N VAL a 15 " --> pdb=" O ARG a 11 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN a 22 " --> pdb=" O SER a 18 " (cutoff:3.500A) Processing helix chain 'a' and resid 25 through 45 removed outlier: 3.674A pdb=" N GLU a 29 " --> pdb=" O SER a 25 " (cutoff:3.500A) Processing helix chain 'a' and resid 51 through 69 removed outlier: 3.890A pdb=" N GLY a 69 " --> pdb=" O ILE a 65 " (cutoff:3.500A) Processing helix chain 'a' and resid 76 through 81 Processing helix chain 'a' and resid 87 through 101 Processing helix chain 'a' and resid 105 through 121 Processing helix chain 'a' and resid 124 through 139 removed outlier: 3.970A pdb=" N VAL a 138 " --> pdb=" O CYS a 134 " (cutoff:3.500A) Processing helix chain 'a' and resid 140 through 148 Processing helix chain 'a' and resid 150 through 156 Processing helix chain 'a' and resid 161 through 179 Processing helix chain 'a' and resid 180 through 183 removed outlier: 3.745A pdb=" N VAL a 183 " --> pdb=" O PRO a 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 180 through 183' Processing helix chain 'a' and resid 188 through 196 removed outlier: 3.862A pdb=" N HIS a 194 " --> pdb=" O SER a 190 " (cutoff:3.500A) Processing helix chain 'a' and resid 201 through 218 Processing helix chain 'a' and resid 219 through 223 removed outlier: 3.890A pdb=" N LYS a 223 " --> pdb=" O GLU a 220 " (cutoff:3.500A) Processing helix chain 'a' and resid 224 through 238 removed outlier: 4.008A pdb=" N LEU a 228 " --> pdb=" O THR a 224 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR a 238 " --> pdb=" O SER a 234 " (cutoff:3.500A) Processing helix chain 'a' and resid 244 through 246 No H-bonds generated for 'chain 'a' and resid 244 through 246' Processing helix chain 'a' and resid 254 through 267 Processing helix chain 'a' and resid 273 through 293 Processing helix chain 'a' and resid 299 through 321 removed outlier: 4.083A pdb=" N SER a 303 " --> pdb=" O LYS a 299 " (cutoff:3.500A) Processing helix chain 'a' and resid 323 through 338 Processing helix chain 'a' and resid 342 through 357 removed outlier: 3.936A pdb=" N ARG a 346 " --> pdb=" O GLU a 342 " (cutoff:3.500A) Processing helix chain 'a' and resid 358 through 361 removed outlier: 6.004A pdb=" N PHE a 361 " --> pdb=" O SER a 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 358 through 361' Processing helix chain 'a' and resid 362 through 368 Processing helix chain 'a' and resid 369 through 380 removed outlier: 3.833A pdb=" N GLU a 380 " --> pdb=" O ALA a 376 " (cutoff:3.500A) Processing helix chain 'a' and resid 383 through 396 removed outlier: 3.630A pdb=" N GLN a 387 " --> pdb=" O VAL a 383 " (cutoff:3.500A) Processing helix chain 'a' and resid 401 through 416 removed outlier: 3.644A pdb=" N ILE a 405 " --> pdb=" O ASN a 401 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR a 415 " --> pdb=" O SER a 411 " (cutoff:3.500A) Processing helix chain 'a' and resid 417 through 419 No H-bonds generated for 'chain 'a' and resid 417 through 419' Processing helix chain 'a' and resid 420 through 435 Processing helix chain 'a' and resid 438 through 453 removed outlier: 3.801A pdb=" N TYR a 442 " --> pdb=" O ASP a 438 " (cutoff:3.500A) Processing helix chain 'a' and resid 460 through 473 removed outlier: 3.784A pdb=" N ASP a 473 " --> pdb=" O VAL a 469 " (cutoff:3.500A) Processing helix chain 'a' and resid 475 through 488 removed outlier: 3.683A pdb=" N GLN a 488 " --> pdb=" O PHE a 484 " (cutoff:3.500A) Processing helix chain 'a' and resid 493 through 508 Processing helix chain 'a' and resid 514 through 517 Processing helix chain 'a' and resid 518 through 531 removed outlier: 3.593A pdb=" N HIS a 531 " --> pdb=" O HIS a 527 " (cutoff:3.500A) Processing helix chain 'a' and resid 534 through 552 removed outlier: 3.914A pdb=" N ASN a 550 " --> pdb=" O ILE a 546 " (cutoff:3.500A) Processing helix chain 'a' and resid 555 through 564 Processing helix chain 'a' and resid 565 through 570 Processing helix chain 'a' and resid 573 through 590 removed outlier: 3.710A pdb=" N ALA a 590 " --> pdb=" O LEU a 586 " (cutoff:3.500A) Processing helix chain 'a' and resid 594 through 599 Processing helix chain 'a' and resid 610 through 620 removed outlier: 3.507A pdb=" N ALA a 614 " --> pdb=" O SER a 610 " (cutoff:3.500A) Processing helix chain 'b' and resid 27 through 44 Processing helix chain 'b' and resid 47 through 49 No H-bonds generated for 'chain 'b' and resid 47 through 49' Processing helix chain 'b' and resid 50 through 58 Processing helix chain 'b' and resid 62 through 78 Processing helix chain 'b' and resid 81 through 86 removed outlier: 3.607A pdb=" N ILE b 85 " --> pdb=" O ASP b 82 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N MET b 86 " --> pdb=" O MET b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 87 through 96 Processing helix chain 'b' and resid 99 through 112 removed outlier: 3.862A pdb=" N CYS b 112 " --> pdb=" O ARG b 108 " (cutoff:3.500A) Processing helix chain 'b' and resid 117 through 129 removed outlier: 4.567A pdb=" N GLU b 124 " --> pdb=" O GLU b 120 " (cutoff:3.500A) Proline residue: b 125 - end of helix Processing helix chain 'b' and resid 134 through 151 removed outlier: 3.888A pdb=" N ASP b 150 " --> pdb=" O ALA b 146 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE b 151 " --> pdb=" O LYS b 147 " (cutoff:3.500A) Processing helix chain 'b' and resid 155 through 170 removed outlier: 4.001A pdb=" N GLN b 159 " --> pdb=" O MET b 155 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA b 170 " --> pdb=" O ARG b 166 " (cutoff:3.500A) Processing helix chain 'b' and resid 173 through 188 Processing helix chain 'b' and resid 202 through 213 Processing helix chain 'b' and resid 215 through 227 Processing helix chain 'b' and resid 233 through 244 removed outlier: 3.845A pdb=" N ALA b 237 " --> pdb=" O ASP b 233 " (cutoff:3.500A) Processing helix chain 'b' and resid 252 through 266 removed outlier: 3.890A pdb=" N VAL b 256 " --> pdb=" O ASN b 252 " (cutoff:3.500A) Processing helix chain 'b' and resid 276 through 291 Proline residue: b 286 - end of helix Processing helix chain 'b' and resid 295 through 313 Processing helix chain 'b' and resid 320 through 325 Processing helix chain 'b' and resid 331 through 345 Processing helix chain 'b' and resid 350 through 362 Processing helix chain 'b' and resid 366 through 384 Processing helix chain 'b' and resid 387 through 400 removed outlier: 3.545A pdb=" N GLN b 400 " --> pdb=" O LEU b 396 " (cutoff:3.500A) Processing helix chain 'b' and resid 403 through 419 removed outlier: 3.538A pdb=" N ARG b 419 " --> pdb=" O ARG b 415 " (cutoff:3.500A) Processing helix chain 'b' and resid 425 through 427 No H-bonds generated for 'chain 'b' and resid 425 through 427' Processing helix chain 'b' and resid 428 through 435 removed outlier: 3.693A pdb=" N LEU b 432 " --> pdb=" O ILE b 428 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASN b 435 " --> pdb=" O THR b 431 " (cutoff:3.500A) Processing helix chain 'b' and resid 441 through 455 Processing helix chain 'b' and resid 461 through 470 Processing helix chain 'b' and resid 477 through 495 Processing helix chain 'b' and resid 502 through 513 Processing helix chain 'b' and resid 516 through 531 Processing helix chain 'b' and resid 533 through 541 Processing helix chain 'b' and resid 556 through 565 removed outlier: 3.616A pdb=" N CYS b 565 " --> pdb=" O ASP b 561 " (cutoff:3.500A) Processing helix chain 'b' and resid 569 through 575 removed outlier: 4.176A pdb=" N VAL b 573 " --> pdb=" O SER b 569 " (cutoff:3.500A) Processing helix chain 'b' and resid 577 through 581 Processing helix chain 'm' and resid 25 through 37 removed outlier: 3.517A pdb=" N VAL m 29 " --> pdb=" O GLY m 25 " (cutoff:3.500A) Processing helix chain 'm' and resid 74 through 94 removed outlier: 3.522A pdb=" N VAL m 78 " --> pdb=" O ASN m 74 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE m 79 " --> pdb=" O ALA m 75 " (cutoff:3.500A) Processing helix chain 'm' and resid 97 through 104 Processing helix chain 'm' and resid 104 through 115 Processing helix chain 'm' and resid 125 through 133 removed outlier: 3.632A pdb=" N THR m 131 " --> pdb=" O GLY m 127 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE m 132 " --> pdb=" O ALA m 128 " (cutoff:3.500A) Processing helix chain 'm' and resid 379 through 383 removed outlier: 3.584A pdb=" N ALA m 382 " --> pdb=" O LYS m 379 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG m 383 " --> pdb=" O LYS m 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 379 through 383' Processing helix chain 'm' and resid 414 through 418 Processing helix chain 's' and resid 24 through 42 removed outlier: 3.661A pdb=" N LYS s 28 " --> pdb=" O ASP s 24 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN s 29 " --> pdb=" O ASP s 25 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL s 41 " --> pdb=" O ALA s 37 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG s 42 " --> pdb=" O VAL s 38 " (cutoff:3.500A) Processing helix chain 's' and resid 77 through 96 Processing helix chain 's' and resid 99 through 106 Processing helix chain 's' and resid 106 through 118 Processing helix chain 's' and resid 128 through 138 Processing sheet with id=AA1, first strand: chain 'A' and resid 248 through 249 Processing sheet with id=AA2, first strand: chain 'M' and resid 14 through 18 removed outlier: 7.047A pdb=" N ILE M 7 " --> pdb=" O LEU M 15 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N SER M 17 " --> pdb=" O LEU M 5 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU M 5 " --> pdb=" O SER M 17 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 116 through 117 removed outlier: 3.796A pdb=" N ASP M 117 " --> pdb=" O TYR M 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 270 through 279 removed outlier: 6.337A pdb=" N GLU M 271 " --> pdb=" O SER M 204 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N SER M 204 " --> pdb=" O GLU M 271 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N GLU M 273 " --> pdb=" O MET M 202 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N MET M 202 " --> pdb=" O GLU M 273 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET M 275 " --> pdb=" O VAL M 200 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER M 193 " --> pdb=" O LEU M 184 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU M 184 " --> pdb=" O SER M 193 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS M 195 " --> pdb=" O ASN M 182 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU M 173 " --> pdb=" O TRP M 421 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ARG M 423 " --> pdb=" O LEU M 173 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU M 175 " --> pdb=" O ARG M 423 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ILE M 425 " --> pdb=" O LEU M 175 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N VAL M 177 " --> pdb=" O ILE M 425 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG M 427 " --> pdb=" O VAL M 177 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N GLU M 179 " --> pdb=" O ARG M 427 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLY M 429 " --> pdb=" O GLU M 179 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL M 181 " --> pdb=" O GLY M 429 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR M 431 " --> pdb=" O VAL M 181 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU M 183 " --> pdb=" O TYR M 431 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N THR M 433 " --> pdb=" O LEU M 183 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N MET M 185 " --> pdb=" O THR M 433 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ARG M 427 " --> pdb=" O VAL M 392 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL M 392 " --> pdb=" O ARG M 427 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLY M 429 " --> pdb=" O PHE M 390 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N PHE M 390 " --> pdb=" O GLY M 429 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TYR M 431 " --> pdb=" O MET M 388 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER M 387 " --> pdb=" O ARG M 323 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLU M 391 " --> pdb=" O LYS M 319 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LYS M 319 " --> pdb=" O GLU M 391 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU M 316 " --> pdb=" O ALA M 359 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA M 359 " --> pdb=" O LEU M 316 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLN M 318 " --> pdb=" O ARG M 357 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ARG M 357 " --> pdb=" O GLN M 318 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 263 through 265 removed outlier: 3.711A pdb=" N ILE M 263 " --> pdb=" O PHE M 214 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE M 265 " --> pdb=" O CYS M 212 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS M 212 " --> pdb=" O PHE M 265 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU M 211 " --> pdb=" O PHE M 407 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE M 407 " --> pdb=" O GLU M 211 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 287 through 294 removed outlier: 3.851A pdb=" N SER M 364 " --> pdb=" O ILE M 307 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER M 367 " --> pdb=" O ILE M 336 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU M 369 " --> pdb=" O GLN M 334 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN M 334 " --> pdb=" O GLU M 369 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N GLY M 332 " --> pdb=" O GLU M 371 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 14 through 19 removed outlier: 7.069A pdb=" N THR S 14 " --> pdb=" O ASN S 9 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ASN S 9 " --> pdb=" O THR S 14 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU S 16 " --> pdb=" O ILE S 7 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N CYS S 70 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE S 5 " --> pdb=" O CYS S 68 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N CYS S 68 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE S 7 " --> pdb=" O TYR S 66 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N TYR S 66 " --> pdb=" O ILE S 7 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS S 56 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL S 50 " --> pdb=" O ILE S 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'a' and resid 248 through 249 Processing sheet with id=AA9, first strand: chain 'm' and resid 14 through 18 removed outlier: 7.046A pdb=" N ILE m 7 " --> pdb=" O LEU m 15 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N SER m 17 " --> pdb=" O LEU m 5 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU m 5 " --> pdb=" O SER m 17 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'm' and resid 116 through 117 removed outlier: 3.796A pdb=" N ASP m 117 " --> pdb=" O TYR m 120 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'm' and resid 270 through 279 removed outlier: 6.337A pdb=" N GLU m 271 " --> pdb=" O SER m 204 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N SER m 204 " --> pdb=" O GLU m 271 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N GLU m 273 " --> pdb=" O MET m 202 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N MET m 202 " --> pdb=" O GLU m 273 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET m 275 " --> pdb=" O VAL m 200 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER m 193 " --> pdb=" O LEU m 184 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU m 184 " --> pdb=" O SER m 193 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS m 195 " --> pdb=" O ASN m 182 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU m 173 " --> pdb=" O TRP m 421 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ARG m 423 " --> pdb=" O LEU m 173 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU m 175 " --> pdb=" O ARG m 423 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ILE m 425 " --> pdb=" O LEU m 175 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N VAL m 177 " --> pdb=" O ILE m 425 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG m 427 " --> pdb=" O VAL m 177 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLU m 179 " --> pdb=" O ARG m 427 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLY m 429 " --> pdb=" O GLU m 179 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL m 181 " --> pdb=" O GLY m 429 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR m 431 " --> pdb=" O VAL m 181 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU m 183 " --> pdb=" O TYR m 431 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N THR m 433 " --> pdb=" O LEU m 183 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N MET m 185 " --> pdb=" O THR m 433 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ARG m 427 " --> pdb=" O VAL m 392 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL m 392 " --> pdb=" O ARG m 427 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLY m 429 " --> pdb=" O PHE m 390 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N PHE m 390 " --> pdb=" O GLY m 429 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TYR m 431 " --> pdb=" O MET m 388 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER m 387 " --> pdb=" O ARG m 323 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLU m 391 " --> pdb=" O LYS m 319 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LYS m 319 " --> pdb=" O GLU m 391 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU m 316 " --> pdb=" O ALA m 359 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA m 359 " --> pdb=" O LEU m 316 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLN m 318 " --> pdb=" O ARG m 357 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ARG m 357 " --> pdb=" O GLN m 318 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'm' and resid 263 through 265 removed outlier: 3.711A pdb=" N ILE m 263 " --> pdb=" O PHE m 214 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE m 265 " --> pdb=" O CYS m 212 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS m 212 " --> pdb=" O PHE m 265 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU m 211 " --> pdb=" O PHE m 407 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE m 407 " --> pdb=" O GLU m 211 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'm' and resid 287 through 294 removed outlier: 3.851A pdb=" N SER m 364 " --> pdb=" O ILE m 307 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER m 367 " --> pdb=" O ILE m 336 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU m 369 " --> pdb=" O GLN m 334 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN m 334 " --> pdb=" O GLU m 369 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N GLY m 332 " --> pdb=" O GLU m 371 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 's' and resid 14 through 19 removed outlier: 7.069A pdb=" N THR s 14 " --> pdb=" O ASN s 9 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ASN s 9 " --> pdb=" O THR s 14 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU s 16 " --> pdb=" O ILE s 7 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N CYS s 70 " --> pdb=" O ARG s 3 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE s 5 " --> pdb=" O CYS s 68 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N CYS s 68 " --> pdb=" O ILE s 5 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE s 7 " --> pdb=" O TYR s 66 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N TYR s 66 " --> pdb=" O ILE s 7 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS s 56 " --> pdb=" O VAL s 71 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL s 50 " --> pdb=" O ILE s 57 " (cutoff:3.500A) 1544 hydrogen bonds defined for protein. 4512 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: 4.66 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7906 1.34 - 1.46: 4542 1.46 - 1.58: 11800 1.58 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 24388 Sorted by residual: bond pdb=" N LEU B 199 " pdb=" CA LEU B 199 " ideal model delta sigma weight residual 1.457 1.470 -0.012 1.29e-02 6.01e+03 8.90e-01 bond pdb=" N LEU b 199 " pdb=" CA LEU b 199 " ideal model delta sigma weight residual 1.457 1.470 -0.012 1.29e-02 6.01e+03 8.90e-01 bond pdb=" C GLN b 202 " pdb=" O GLN b 202 " ideal model delta sigma weight residual 1.235 1.246 -0.011 1.26e-02 6.30e+03 7.02e-01 bond pdb=" CD LYS A 56 " pdb=" CE LYS A 56 " ideal model delta sigma weight residual 1.520 1.495 0.025 3.00e-02 1.11e+03 6.80e-01 bond pdb=" C GLN B 202 " pdb=" O GLN B 202 " ideal model delta sigma weight residual 1.235 1.246 -0.010 1.26e-02 6.30e+03 6.79e-01 ... (remaining 24383 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 32898 1.82 - 3.64: 438 3.64 - 5.46: 52 5.46 - 7.27: 10 7.27 - 9.09: 2 Bond angle restraints: 33400 Sorted by residual: angle pdb=" N VAL a 555 " pdb=" CA VAL a 555 " pdb=" C VAL a 555 " ideal model delta sigma weight residual 112.29 107.75 4.54 9.40e-01 1.13e+00 2.33e+01 angle pdb=" N VAL A 555 " pdb=" CA VAL A 555 " pdb=" C VAL A 555 " ideal model delta sigma weight residual 112.29 107.80 4.49 9.40e-01 1.13e+00 2.28e+01 angle pdb=" C SER A 591 " pdb=" N THR A 592 " pdb=" CA THR A 592 " ideal model delta sigma weight residual 121.54 127.72 -6.18 1.91e+00 2.74e-01 1.05e+01 angle pdb=" C SER a 591 " pdb=" N THR a 592 " pdb=" CA THR a 592 " ideal model delta sigma weight residual 121.54 127.72 -6.18 1.91e+00 2.74e-01 1.05e+01 angle pdb=" C PRO B 201 " pdb=" N GLN B 202 " pdb=" CA GLN B 202 " ideal model delta sigma weight residual 121.54 127.24 -5.70 1.91e+00 2.74e-01 8.90e+00 ... (remaining 33395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 13452 17.76 - 35.51: 920 35.51 - 53.27: 146 53.27 - 71.03: 30 71.03 - 88.78: 12 Dihedral angle restraints: 14560 sinusoidal: 4470 harmonic: 10090 Sorted by residual: dihedral pdb=" CA SER A 458 " pdb=" C SER A 458 " pdb=" N GLU A 459 " pdb=" CA GLU A 459 " ideal model delta harmonic sigma weight residual 180.00 158.48 21.52 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA SER a 458 " pdb=" C SER a 458 " pdb=" N GLU a 459 " pdb=" CA GLU a 459 " ideal model delta harmonic sigma weight residual 180.00 158.48 21.52 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA LYS A 378 " pdb=" C LYS A 378 " pdb=" N THR A 379 " pdb=" CA THR A 379 " ideal model delta harmonic sigma weight residual -180.00 -163.41 -16.59 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 14557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2848 0.035 - 0.070: 994 0.070 - 0.106: 250 0.106 - 0.141: 74 0.141 - 0.176: 4 Chirality restraints: 4170 Sorted by residual: chirality pdb=" CB THR A 238 " pdb=" CA THR A 238 " pdb=" OG1 THR A 238 " pdb=" CG2 THR A 238 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.75e-01 chirality pdb=" CB THR a 238 " pdb=" CA THR a 238 " pdb=" OG1 THR a 238 " pdb=" CG2 THR a 238 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.63e-01 chirality pdb=" CA ILE S 58 " pdb=" N ILE S 58 " pdb=" C ILE S 58 " pdb=" CB ILE S 58 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.46e-01 ... (remaining 4167 not shown) Planarity restraints: 4260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL m 392 " -0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO m 393 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO m 393 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO m 393 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL M 392 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO M 393 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO M 393 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO M 393 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 269 " 0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO A 270 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 270 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 270 " 0.020 5.00e-02 4.00e+02 ... (remaining 4257 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 217 2.66 - 3.22: 23126 3.22 - 3.78: 36709 3.78 - 4.34: 45125 4.34 - 4.90: 76723 Nonbonded interactions: 181900 Sorted by model distance: nonbonded pdb=" OD1 ASP a 417 " pdb=" OG SER a 419 " model vdw 2.103 3.040 nonbonded pdb=" OD1 ASP A 417 " pdb=" OG SER A 419 " model vdw 2.103 3.040 nonbonded pdb=" OH TYR A 95 " pdb=" OD2 ASP A 119 " model vdw 2.194 3.040 nonbonded pdb=" OH TYR a 95 " pdb=" OD2 ASP a 119 " model vdw 2.194 3.040 nonbonded pdb=" O VAL b 301 " pdb=" ND2 ASN b 305 " model vdw 2.217 3.120 ... (remaining 181895 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'S' selection = chain 's' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.820 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: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.930 Find NCS groups from input model: 0.230 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24388 Z= 0.123 Angle : 0.533 9.092 33400 Z= 0.300 Chirality : 0.040 0.176 4170 Planarity : 0.003 0.038 4260 Dihedral : 12.887 88.783 7972 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.44 % Favored : 95.50 % Rotamer: Outliers : 0.10 % Allowed : 0.14 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.15), residues: 3380 helix: 1.90 (0.12), residues: 1934 sheet: -0.13 (0.29), residues: 330 loop : -1.53 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG m 199 TYR 0.015 0.001 TYR a 583 PHE 0.013 0.001 PHE A 552 TRP 0.014 0.001 TRP A 462 HIS 0.003 0.001 HIS s 85 Details of bonding type rmsd covalent geometry : bond 0.00258 (24388) covalent geometry : angle 0.53267 (33400) hydrogen bonds : bond 0.14639 ( 1544) hydrogen bonds : angle 5.87787 ( 4512) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 244 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 246 average time/residue: 0.1320 time to fit residues: 53.7874 Evaluate side-chains 184 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 197 optimal weight: 0.0670 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.2980 chunk 298 optimal weight: 8.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 ASN M 38 HIS a 22 ASN ** a 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 179 ASN m 38 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.176430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.175615 restraints weight = 40820.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.175426 restraints weight = 52609.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.175357 restraints weight = 60928.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.175308 restraints weight = 59942.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.175284 restraints weight = 55523.148| |-----------------------------------------------------------------------------| r_work (final): 0.4409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24388 Z= 0.133 Angle : 0.516 11.865 33400 Z= 0.272 Chirality : 0.040 0.164 4170 Planarity : 0.004 0.039 4260 Dihedral : 3.675 19.242 3604 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.67 % Favored : 95.27 % Rotamer: Outliers : 0.96 % Allowed : 8.37 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.15), residues: 3380 helix: 1.93 (0.12), residues: 1954 sheet: -0.18 (0.29), residues: 332 loop : -1.45 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 199 TYR 0.015 0.001 TYR a 463 PHE 0.018 0.001 PHE B 369 TRP 0.012 0.001 TRP A 462 HIS 0.006 0.001 HIS s 85 Details of bonding type rmsd covalent geometry : bond 0.00306 (24388) covalent geometry : angle 0.51623 (33400) hydrogen bonds : bond 0.03772 ( 1544) hydrogen bonds : angle 4.56246 ( 4512) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 201 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.7854 (tp) cc_final: 0.7599 (tp) REVERT: A 151 ILE cc_start: 0.8430 (mm) cc_final: 0.8165 (mm) REVERT: a 62 LEU cc_start: 0.7858 (tp) cc_final: 0.7600 (tp) outliers start: 20 outliers final: 8 residues processed: 211 average time/residue: 0.1301 time to fit residues: 46.2114 Evaluate side-chains 181 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 173 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain S residue 97 ASN Chi-restraints excluded: chain a residue 455 ASP Chi-restraints excluded: chain a residue 456 TYR Chi-restraints excluded: chain b residue 321 ILE Chi-restraints excluded: chain s residue 97 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 309 optimal weight: 0.0020 chunk 92 optimal weight: 0.5980 chunk 315 optimal weight: 10.0000 chunk 313 optimal weight: 0.6980 chunk 290 optimal weight: 0.9980 chunk 171 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 287 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 70 optimal weight: 0.0870 chunk 174 optimal weight: 0.5980 overall best weight: 0.3966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 ASN M 38 HIS ** a 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 179 ASN m 38 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.175814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.173839 restraints weight = 40730.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.173404 restraints weight = 57833.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.173147 restraints weight = 71087.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.172260 restraints weight = 67018.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.168430 restraints weight = 74972.542| |-----------------------------------------------------------------------------| r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24388 Z= 0.110 Angle : 0.480 10.403 33400 Z= 0.256 Chirality : 0.039 0.157 4170 Planarity : 0.003 0.037 4260 Dihedral : 3.592 19.079 3604 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.34 % Allowed : 10.72 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.15), residues: 3380 helix: 1.98 (0.12), residues: 1974 sheet: -0.10 (0.29), residues: 324 loop : -1.53 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 423 TYR 0.021 0.001 TYR a 583 PHE 0.009 0.001 PHE a 530 TRP 0.011 0.001 TRP a 462 HIS 0.005 0.001 HIS s 85 Details of bonding type rmsd covalent geometry : bond 0.00245 (24388) covalent geometry : angle 0.48049 (33400) hydrogen bonds : bond 0.03384 ( 1544) hydrogen bonds : angle 4.20133 ( 4512) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.7798 (tp) cc_final: 0.7501 (tp) REVERT: A 185 MET cc_start: 0.8159 (mmt) cc_final: 0.7902 (mmt) REVERT: a 62 LEU cc_start: 0.7804 (tp) cc_final: 0.7516 (tp) REVERT: a 185 MET cc_start: 0.8140 (mmt) cc_final: 0.7885 (mmt) outliers start: 28 outliers final: 16 residues processed: 211 average time/residue: 0.1313 time to fit residues: 46.4672 Evaluate side-chains 198 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 97 ASN Chi-restraints excluded: chain a residue 135 ILE Chi-restraints excluded: chain a residue 455 ASP Chi-restraints excluded: chain a residue 456 TYR Chi-restraints excluded: chain a residue 457 VAL Chi-restraints excluded: chain a residue 483 VAL Chi-restraints excluded: chain b residue 321 ILE Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 97 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 232 optimal weight: 30.0000 chunk 110 optimal weight: 0.5980 chunk 70 optimal weight: 0.0570 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 325 optimal weight: 0.9990 chunk 253 optimal weight: 0.7980 chunk 310 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 227 optimal weight: 3.9990 chunk 292 optimal weight: 2.9990 overall best weight: 0.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 38 HIS ** a 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 38 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.173258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.170613 restraints weight = 40672.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.169638 restraints weight = 65586.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.169127 restraints weight = 75727.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.168529 restraints weight = 75787.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.168346 restraints weight = 71603.883| |-----------------------------------------------------------------------------| r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24388 Z= 0.151 Angle : 0.517 10.102 33400 Z= 0.272 Chirality : 0.040 0.147 4170 Planarity : 0.003 0.037 4260 Dihedral : 3.709 19.312 3604 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.06 % Allowed : 11.96 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.15), residues: 3380 helix: 1.91 (0.12), residues: 1966 sheet: -0.09 (0.28), residues: 322 loop : -1.47 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG m 423 TYR 0.018 0.001 TYR a 583 PHE 0.013 0.001 PHE S 118 TRP 0.009 0.001 TRP a 462 HIS 0.004 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00358 (24388) covalent geometry : angle 0.51692 (33400) hydrogen bonds : bond 0.03544 ( 1544) hydrogen bonds : angle 4.08568 ( 4512) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 196 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.7810 (tp) cc_final: 0.7492 (tp) REVERT: M 176 ASP cc_start: 0.6153 (m-30) cc_final: 0.5915 (m-30) REVERT: a 62 LEU cc_start: 0.7805 (tp) cc_final: 0.7493 (tp) REVERT: a 546 ILE cc_start: 0.8892 (tp) cc_final: 0.8614 (tp) outliers start: 43 outliers final: 21 residues processed: 225 average time/residue: 0.1273 time to fit residues: 48.6765 Evaluate side-chains 206 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain M residue 366 ILE Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain a residue 135 ILE Chi-restraints excluded: chain a residue 456 TYR Chi-restraints excluded: chain a residue 457 VAL Chi-restraints excluded: chain a residue 483 VAL Chi-restraints excluded: chain b residue 321 ILE Chi-restraints excluded: chain b residue 399 ILE Chi-restraints excluded: chain m residue 366 ILE Chi-restraints excluded: chain s residue 49 PHE Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 131 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 226 optimal weight: 0.7980 chunk 269 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 294 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 287 optimal weight: 0.4980 chunk 234 optimal weight: 5.9990 chunk 203 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 299 GLN M 38 HIS M 122 GLN ** a 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 299 GLN m 38 HIS m 122 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.168037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.165303 restraints weight = 40952.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.165163 restraints weight = 45617.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.164217 restraints weight = 55827.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.163901 restraints weight = 63754.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.163520 restraints weight = 63217.887| |-----------------------------------------------------------------------------| r_work (final): 0.4320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24388 Z= 0.165 Angle : 0.533 9.391 33400 Z= 0.279 Chirality : 0.041 0.156 4170 Planarity : 0.003 0.038 4260 Dihedral : 3.807 19.934 3604 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.44 % Allowed : 14.07 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.15), residues: 3380 helix: 1.85 (0.12), residues: 1962 sheet: -0.10 (0.28), residues: 322 loop : -1.50 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG m 423 TYR 0.020 0.001 TYR a 463 PHE 0.014 0.001 PHE s 118 TRP 0.009 0.001 TRP A 462 HIS 0.004 0.001 HIS a 200 Details of bonding type rmsd covalent geometry : bond 0.00398 (24388) covalent geometry : angle 0.53258 (33400) hydrogen bonds : bond 0.03522 ( 1544) hydrogen bonds : angle 4.08477 ( 4512) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 189 time to evaluate : 0.929 Fit side-chains REVERT: A 62 LEU cc_start: 0.7807 (tp) cc_final: 0.7489 (tp) REVERT: A 551 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8083 (tt) REVERT: B 361 TYR cc_start: 0.6755 (m-10) cc_final: 0.6521 (m-10) REVERT: M 1 MET cc_start: 0.7305 (ttm) cc_final: 0.6617 (ttp) REVERT: a 62 LEU cc_start: 0.7794 (tp) cc_final: 0.7451 (tp) REVERT: a 551 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7954 (tt) REVERT: b 361 TYR cc_start: 0.6744 (m-10) cc_final: 0.6468 (m-10) outliers start: 51 outliers final: 23 residues processed: 229 average time/residue: 0.1244 time to fit residues: 48.4425 Evaluate side-chains 208 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 366 ILE Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain a residue 135 ILE Chi-restraints excluded: chain a residue 455 ASP Chi-restraints excluded: chain a residue 456 TYR Chi-restraints excluded: chain a residue 551 LEU Chi-restraints excluded: chain a residue 565 SER Chi-restraints excluded: chain b residue 321 ILE Chi-restraints excluded: chain b residue 342 MET Chi-restraints excluded: chain b residue 399 ILE Chi-restraints excluded: chain b residue 403 VAL Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 366 ILE Chi-restraints excluded: chain s residue 49 PHE Chi-restraints excluded: chain s residue 50 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 330 optimal weight: 0.3980 chunk 306 optimal weight: 20.0000 chunk 210 optimal weight: 0.6980 chunk 294 optimal weight: 3.9990 chunk 202 optimal weight: 0.6980 chunk 323 optimal weight: 7.9990 chunk 237 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 135 optimal weight: 20.0000 chunk 185 optimal weight: 1.9990 chunk 278 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN M 38 HIS a 22 ASN m 38 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.168190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.164969 restraints weight = 41137.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.159018 restraints weight = 61239.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.156507 restraints weight = 70754.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.156753 restraints weight = 93451.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.156798 restraints weight = 65374.829| |-----------------------------------------------------------------------------| r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24388 Z= 0.151 Angle : 0.518 9.021 33400 Z= 0.272 Chirality : 0.040 0.157 4170 Planarity : 0.003 0.040 4260 Dihedral : 3.816 20.241 3604 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.54 % Allowed : 15.74 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.15), residues: 3380 helix: 1.87 (0.12), residues: 1962 sheet: -0.10 (0.28), residues: 322 loop : -1.48 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG m 423 TYR 0.024 0.001 TYR a 463 PHE 0.012 0.001 PHE s 118 TRP 0.011 0.001 TRP a 462 HIS 0.004 0.001 HIS S 46 Details of bonding type rmsd covalent geometry : bond 0.00364 (24388) covalent geometry : angle 0.51751 (33400) hydrogen bonds : bond 0.03435 ( 1544) hydrogen bonds : angle 4.03155 ( 4512) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 179 time to evaluate : 0.840 Fit side-chains REVERT: A 62 LEU cc_start: 0.7792 (tp) cc_final: 0.7451 (tp) REVERT: A 551 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8095 (tt) REVERT: B 361 TYR cc_start: 0.6919 (m-10) cc_final: 0.6579 (m-10) REVERT: a 62 LEU cc_start: 0.7796 (tp) cc_final: 0.7458 (tp) REVERT: a 551 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7875 (tt) REVERT: b 361 TYR cc_start: 0.6876 (m-10) cc_final: 0.6624 (m-10) outliers start: 53 outliers final: 29 residues processed: 220 average time/residue: 0.1272 time to fit residues: 47.5829 Evaluate side-chains 206 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 366 ILE Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 91 LEU Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain a residue 135 ILE Chi-restraints excluded: chain a residue 201 LEU Chi-restraints excluded: chain a residue 320 HIS Chi-restraints excluded: chain a residue 456 TYR Chi-restraints excluded: chain a residue 520 LEU Chi-restraints excluded: chain a residue 551 LEU Chi-restraints excluded: chain a residue 565 SER Chi-restraints excluded: chain b residue 321 ILE Chi-restraints excluded: chain b residue 399 ILE Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 366 ILE Chi-restraints excluded: chain s residue 49 PHE Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 91 LEU Chi-restraints excluded: chain s residue 97 ASN Chi-restraints excluded: chain s residue 131 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 113 optimal weight: 0.9990 chunk 191 optimal weight: 0.5980 chunk 140 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 90 optimal weight: 0.3980 chunk 335 optimal weight: 0.6980 chunk 259 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 188 optimal weight: 1.9990 chunk 184 optimal weight: 0.5980 chunk 71 optimal weight: 20.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.169527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.166618 restraints weight = 40947.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.165333 restraints weight = 74096.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.164839 restraints weight = 79018.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.163816 restraints weight = 82914.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.163510 restraints weight = 82702.490| |-----------------------------------------------------------------------------| r_work (final): 0.4305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24388 Z= 0.120 Angle : 0.489 9.580 33400 Z= 0.260 Chirality : 0.040 0.158 4170 Planarity : 0.003 0.039 4260 Dihedral : 3.730 19.937 3604 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.91 % Allowed : 16.94 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.15), residues: 3380 helix: 1.94 (0.12), residues: 1970 sheet: -0.05 (0.28), residues: 322 loop : -1.43 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 423 TYR 0.026 0.001 TYR a 463 PHE 0.010 0.001 PHE a 530 TRP 0.012 0.001 TRP a 462 HIS 0.003 0.001 HIS S 46 Details of bonding type rmsd covalent geometry : bond 0.00280 (24388) covalent geometry : angle 0.48870 (33400) hydrogen bonds : bond 0.03206 ( 1544) hydrogen bonds : angle 3.93714 ( 4512) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 185 time to evaluate : 0.921 Fit side-chains REVERT: A 62 LEU cc_start: 0.7732 (tp) cc_final: 0.7341 (tp) REVERT: A 551 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8083 (tt) REVERT: B 361 TYR cc_start: 0.6785 (m-10) cc_final: 0.6540 (m-10) REVERT: a 62 LEU cc_start: 0.7730 (tp) cc_final: 0.7350 (tp) REVERT: a 551 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7838 (tt) REVERT: b 361 TYR cc_start: 0.6805 (m-10) cc_final: 0.6573 (m-10) outliers start: 40 outliers final: 33 residues processed: 218 average time/residue: 0.1310 time to fit residues: 48.5122 Evaluate side-chains 213 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain S residue 91 LEU Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain a residue 135 ILE Chi-restraints excluded: chain a residue 201 LEU Chi-restraints excluded: chain a residue 440 THR Chi-restraints excluded: chain a residue 456 TYR Chi-restraints excluded: chain a residue 457 VAL Chi-restraints excluded: chain a residue 520 LEU Chi-restraints excluded: chain a residue 551 LEU Chi-restraints excluded: chain a residue 565 SER Chi-restraints excluded: chain b residue 321 ILE Chi-restraints excluded: chain b residue 399 ILE Chi-restraints excluded: chain b residue 403 VAL Chi-restraints excluded: chain b residue 563 LEU Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain s residue 49 PHE Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 90 VAL Chi-restraints excluded: chain s residue 91 LEU Chi-restraints excluded: chain s residue 131 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 96 optimal weight: 0.5980 chunk 191 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 271 optimal weight: 9.9990 chunk 210 optimal weight: 0.3980 chunk 261 optimal weight: 1.9990 chunk 184 optimal weight: 0.4980 chunk 101 optimal weight: 0.9990 chunk 250 optimal weight: 20.0000 chunk 217 optimal weight: 2.9990 chunk 224 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 38 HIS m 38 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.173791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.172670 restraints weight = 40385.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.172406 restraints weight = 65839.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.172243 restraints weight = 74698.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.172079 restraints weight = 67498.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.171932 restraints weight = 71200.561| |-----------------------------------------------------------------------------| r_work (final): 0.4369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24388 Z= 0.127 Angle : 0.492 8.924 33400 Z= 0.260 Chirality : 0.040 0.144 4170 Planarity : 0.003 0.038 4260 Dihedral : 3.697 19.475 3604 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.06 % Allowed : 17.22 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.15), residues: 3380 helix: 1.95 (0.12), residues: 1970 sheet: -0.04 (0.28), residues: 322 loop : -1.42 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG m 423 TYR 0.026 0.001 TYR a 463 PHE 0.011 0.001 PHE a 530 TRP 0.011 0.001 TRP a 462 HIS 0.003 0.001 HIS S 46 Details of bonding type rmsd covalent geometry : bond 0.00301 (24388) covalent geometry : angle 0.49195 (33400) hydrogen bonds : bond 0.03218 ( 1544) hydrogen bonds : angle 3.90308 ( 4512) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 181 time to evaluate : 0.883 Fit side-chains REVERT: A 62 LEU cc_start: 0.7703 (tp) cc_final: 0.7438 (tp) REVERT: A 551 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8026 (tt) REVERT: a 62 LEU cc_start: 0.7708 (tp) cc_final: 0.7441 (tp) REVERT: a 551 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7845 (tt) outliers start: 43 outliers final: 36 residues processed: 214 average time/residue: 0.1274 time to fit residues: 46.4312 Evaluate side-chains 213 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 175 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 366 ILE Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain S residue 91 LEU Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain a residue 135 ILE Chi-restraints excluded: chain a residue 201 LEU Chi-restraints excluded: chain a residue 440 THR Chi-restraints excluded: chain a residue 456 TYR Chi-restraints excluded: chain a residue 457 VAL Chi-restraints excluded: chain a residue 520 LEU Chi-restraints excluded: chain a residue 551 LEU Chi-restraints excluded: chain a residue 565 SER Chi-restraints excluded: chain b residue 321 ILE Chi-restraints excluded: chain b residue 399 ILE Chi-restraints excluded: chain b residue 403 VAL Chi-restraints excluded: chain b residue 563 LEU Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 366 ILE Chi-restraints excluded: chain s residue 49 PHE Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 90 VAL Chi-restraints excluded: chain s residue 91 LEU Chi-restraints excluded: chain s residue 131 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 260 optimal weight: 0.9980 chunk 182 optimal weight: 0.8980 chunk 81 optimal weight: 20.0000 chunk 251 optimal weight: 5.9990 chunk 270 optimal weight: 0.2980 chunk 262 optimal weight: 4.9990 chunk 245 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 38 HIS m 38 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.173161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.171799 restraints weight = 40438.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.171579 restraints weight = 65957.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.171397 restraints weight = 69942.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.171215 restraints weight = 70042.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.171057 restraints weight = 70361.449| |-----------------------------------------------------------------------------| r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24388 Z= 0.141 Angle : 0.506 8.663 33400 Z= 0.267 Chirality : 0.040 0.143 4170 Planarity : 0.003 0.038 4260 Dihedral : 3.715 19.415 3604 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.30 % Allowed : 17.37 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.15), residues: 3380 helix: 1.91 (0.12), residues: 1970 sheet: -0.02 (0.28), residues: 322 loop : -1.42 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 423 TYR 0.027 0.001 TYR a 463 PHE 0.011 0.001 PHE S 118 TRP 0.011 0.001 TRP a 462 HIS 0.003 0.001 HIS S 46 Details of bonding type rmsd covalent geometry : bond 0.00338 (24388) covalent geometry : angle 0.50627 (33400) hydrogen bonds : bond 0.03312 ( 1544) hydrogen bonds : angle 3.93289 ( 4512) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 181 time to evaluate : 0.892 Fit side-chains REVERT: A 62 LEU cc_start: 0.7761 (tp) cc_final: 0.7396 (tp) REVERT: A 551 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8043 (tt) REVERT: B 361 TYR cc_start: 0.6521 (m-10) cc_final: 0.6067 (m-80) REVERT: a 62 LEU cc_start: 0.7766 (tp) cc_final: 0.7405 (tp) REVERT: a 551 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7860 (tt) REVERT: b 361 TYR cc_start: 0.6531 (m-10) cc_final: 0.6067 (m-80) outliers start: 48 outliers final: 37 residues processed: 220 average time/residue: 0.1264 time to fit residues: 47.3258 Evaluate side-chains 216 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 366 ILE Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain S residue 91 LEU Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain a residue 135 ILE Chi-restraints excluded: chain a residue 201 LEU Chi-restraints excluded: chain a residue 320 HIS Chi-restraints excluded: chain a residue 440 THR Chi-restraints excluded: chain a residue 455 ASP Chi-restraints excluded: chain a residue 456 TYR Chi-restraints excluded: chain a residue 520 LEU Chi-restraints excluded: chain a residue 551 LEU Chi-restraints excluded: chain a residue 562 VAL Chi-restraints excluded: chain a residue 565 SER Chi-restraints excluded: chain b residue 321 ILE Chi-restraints excluded: chain b residue 399 ILE Chi-restraints excluded: chain b residue 403 VAL Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 366 ILE Chi-restraints excluded: chain s residue 49 PHE Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 90 VAL Chi-restraints excluded: chain s residue 91 LEU Chi-restraints excluded: chain s residue 131 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 203 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 308 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 205 optimal weight: 0.5980 chunk 319 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 325 optimal weight: 0.6980 chunk 183 optimal weight: 0.6980 chunk 299 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 38 HIS m 38 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.169485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.166134 restraints weight = 40840.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.165882 restraints weight = 55604.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.165343 restraints weight = 57772.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.165063 restraints weight = 61267.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.164826 restraints weight = 62094.515| |-----------------------------------------------------------------------------| r_work (final): 0.4278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24388 Z= 0.126 Angle : 0.499 11.386 33400 Z= 0.264 Chirality : 0.040 0.145 4170 Planarity : 0.003 0.039 4260 Dihedral : 3.681 19.268 3604 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.87 % Allowed : 17.75 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.15), residues: 3380 helix: 1.95 (0.12), residues: 1972 sheet: -0.10 (0.28), residues: 330 loop : -1.37 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 423 TYR 0.026 0.001 TYR a 463 PHE 0.010 0.001 PHE B 369 TRP 0.012 0.001 TRP a 462 HIS 0.003 0.001 HIS s 46 Details of bonding type rmsd covalent geometry : bond 0.00300 (24388) covalent geometry : angle 0.49912 (33400) hydrogen bonds : bond 0.03204 ( 1544) hydrogen bonds : angle 3.88886 ( 4512) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 0.917 Fit side-chains REVERT: A 62 LEU cc_start: 0.7759 (tp) cc_final: 0.7413 (tp) REVERT: A 551 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8092 (tt) REVERT: a 62 LEU cc_start: 0.7755 (tp) cc_final: 0.7412 (tp) REVERT: a 551 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7906 (tt) outliers start: 39 outliers final: 36 residues processed: 207 average time/residue: 0.1302 time to fit residues: 45.6674 Evaluate side-chains 213 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 175 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 366 ILE Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain S residue 91 LEU Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain a residue 135 ILE Chi-restraints excluded: chain a residue 201 LEU Chi-restraints excluded: chain a residue 440 THR Chi-restraints excluded: chain a residue 455 ASP Chi-restraints excluded: chain a residue 456 TYR Chi-restraints excluded: chain a residue 520 LEU Chi-restraints excluded: chain a residue 551 LEU Chi-restraints excluded: chain a residue 562 VAL Chi-restraints excluded: chain a residue 565 SER Chi-restraints excluded: chain b residue 321 ILE Chi-restraints excluded: chain b residue 399 ILE Chi-restraints excluded: chain b residue 403 VAL Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 366 ILE Chi-restraints excluded: chain s residue 49 PHE Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 90 VAL Chi-restraints excluded: chain s residue 91 LEU Chi-restraints excluded: chain s residue 131 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 144 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 279 optimal weight: 0.6980 chunk 336 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 218 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 328 optimal weight: 0.2980 chunk 176 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 38 HIS m 38 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.169633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.166476 restraints weight = 40781.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.165896 restraints weight = 65398.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.165186 restraints weight = 69890.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.164924 restraints weight = 71841.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.164777 restraints weight = 63933.859| |-----------------------------------------------------------------------------| r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24388 Z= 0.125 Angle : 0.496 11.402 33400 Z= 0.263 Chirality : 0.040 0.144 4170 Planarity : 0.003 0.038 4260 Dihedral : 3.679 19.109 3604 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.11 % Allowed : 17.66 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.15), residues: 3380 helix: 1.94 (0.12), residues: 1978 sheet: -0.10 (0.27), residues: 330 loop : -1.34 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 33 TYR 0.026 0.001 TYR a 463 PHE 0.012 0.001 PHE B 369 TRP 0.012 0.001 TRP a 462 HIS 0.003 0.001 HIS S 46 Details of bonding type rmsd covalent geometry : bond 0.00297 (24388) covalent geometry : angle 0.49636 (33400) hydrogen bonds : bond 0.03212 ( 1544) hydrogen bonds : angle 3.87420 ( 4512) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2581.23 seconds wall clock time: 45 minutes 51.78 seconds (2751.78 seconds total)