Starting phenix.real_space_refine on Fri Sep 27 11:35:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8igg_35432/09_2024/8igg_35432.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8igg_35432/09_2024/8igg_35432.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8igg_35432/09_2024/8igg_35432.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8igg_35432/09_2024/8igg_35432.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8igg_35432/09_2024/8igg_35432.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8igg_35432/09_2024/8igg_35432.cif" } resolution = 4.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 50 5.16 5 C 10002 2.51 5 N 2892 2.21 5 O 3054 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 15998 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3985 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 23, 'TRANS': 487} Chain breaks: 3 Chain: "B" Number of atoms: 4014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4014 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 491} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, E Time building chain proxies: 12.83, per 1000 atoms: 0.80 Number of scatterers: 15998 At special positions: 0 Unit cell: (148.75, 126.25, 87.5, 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 50 16.00 O 3054 8.00 N 2892 7.00 C 10002 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: 3.87 Conformation dependent library (CDL) restraints added in 2.1 seconds 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3800 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 22 sheets defined 42.2% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'E' and resid 50 through 55 removed outlier: 3.908A pdb=" N PHE E 54 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR E 55 " --> pdb=" O ASN E 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 50 through 55' Processing helix chain 'E' and resid 65 through 84 removed outlier: 3.826A pdb=" N GLU E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN E 84 " --> pdb=" O GLN E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 102 removed outlier: 3.846A pdb=" N HIS E 101 " --> pdb=" O ARG E 98 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN E 102 " --> pdb=" O ASP E 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 98 through 102' Processing helix chain 'E' and resid 163 through 179 Processing helix chain 'E' and resid 198 through 201 removed outlier: 3.513A pdb=" N ASP E 201 " --> pdb=" O VAL E 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 198 through 201' Processing helix chain 'E' and resid 202 through 226 Processing helix chain 'E' and resid 231 through 235 Processing helix chain 'E' and resid 302 through 311 removed outlier: 3.892A pdb=" N GLN E 306 " --> pdb=" O THR E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 351 Processing helix chain 'E' and resid 352 through 367 removed outlier: 4.432A pdb=" N SER E 356 " --> pdb=" O ALA E 353 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N GLY E 359 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N TRP E 362 " --> pdb=" O GLY E 359 " (cutoff:3.500A) Proline residue: E 365 - end of helix Processing helix chain 'E' and resid 378 through 384 removed outlier: 3.565A pdb=" N ALA E 381 " --> pdb=" O ASP E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 410 Processing helix chain 'E' and resid 428 through 439 removed outlier: 3.848A pdb=" N LEU E 434 " --> pdb=" O GLN E 430 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN E 435 " --> pdb=" O MET E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 460 Processing helix chain 'E' and resid 462 through 466 Processing helix chain 'E' and resid 497 through 499 No H-bonds generated for 'chain 'E' and resid 497 through 499' Processing helix chain 'E' and resid 501 through 509 Processing helix chain 'E' and resid 511 through 523 Processing helix chain 'E' and resid 528 through 543 Processing helix chain 'E' and resid 560 through 576 removed outlier: 3.656A pdb=" N ILE E 564 " --> pdb=" O ASN E 560 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG E 569 " --> pdb=" O GLU E 565 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU E 576 " --> pdb=" O ALA E 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 82 Processing helix chain 'A' and resid 157 through 162 removed outlier: 3.616A pdb=" N PHE A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 177 Processing helix chain 'A' and resid 202 through 222 removed outlier: 3.546A pdb=" N LEU A 221 " --> pdb=" O CYS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 removed outlier: 4.245A pdb=" N LYS A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY A 237 " --> pdb=" O ALA A 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 232 through 237' Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.546A pdb=" N PHE A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 364 removed outlier: 3.866A pdb=" N ALA A 361 " --> pdb=" O HIS A 358 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N TRP A 362 " --> pdb=" O GLY A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 386 removed outlier: 4.031A pdb=" N ALA A 381 " --> pdb=" O ASP A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 412 Processing helix chain 'A' and resid 428 through 439 removed outlier: 4.804A pdb=" N LEU A 434 " --> pdb=" O GLN A 430 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN A 435 " --> pdb=" O MET A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 457 Processing helix chain 'A' and resid 462 through 467 removed outlier: 3.983A pdb=" N PHE A 466 " --> pdb=" O GLY A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 499 removed outlier: 3.614A pdb=" N LEU A 499 " --> pdb=" O ARG A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 509 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 528 through 544 removed outlier: 3.684A pdb=" N ARG A 532 " --> pdb=" O HIS A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 575 removed outlier: 3.753A pdb=" N ILE A 564 " --> pdb=" O ASN A 560 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 601 removed outlier: 3.618A pdb=" N ASN A 601 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 55 removed outlier: 3.908A pdb=" N PHE B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR B 55 " --> pdb=" O ASN B 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 50 through 55' Processing helix chain 'B' and resid 65 through 84 removed outlier: 3.826A pdb=" N GLU B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN B 84 " --> pdb=" O GLN B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 102 removed outlier: 3.846A pdb=" N HIS B 101 " --> pdb=" O ARG B 98 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN B 102 " --> pdb=" O ASP B 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 98 through 102' Processing helix chain 'B' and resid 163 through 179 Processing helix chain 'B' and resid 198 through 201 removed outlier: 3.513A pdb=" N ASP B 201 " --> pdb=" O VAL B 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 201' Processing helix chain 'B' and resid 202 through 226 Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 302 through 311 removed outlier: 3.892A pdb=" N GLN B 306 " --> pdb=" O THR B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 351 Processing helix chain 'B' and resid 352 through 367 removed outlier: 4.432A pdb=" N SER B 356 " --> pdb=" O ALA B 353 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N GLY B 359 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N TRP B 362 " --> pdb=" O GLY B 359 " (cutoff:3.500A) Proline residue: B 365 - end of helix Processing helix chain 'B' and resid 378 through 384 removed outlier: 3.565A pdb=" N ALA B 381 " --> pdb=" O ASP B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 410 Processing helix chain 'B' and resid 428 through 439 removed outlier: 3.848A pdb=" N LEU B 434 " --> pdb=" O GLN B 430 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN B 435 " --> pdb=" O MET B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 460 Processing helix chain 'B' and resid 462 through 466 Processing helix chain 'B' and resid 497 through 499 No H-bonds generated for 'chain 'B' and resid 497 through 499' Processing helix chain 'B' and resid 501 through 509 Processing helix chain 'B' and resid 511 through 523 Processing helix chain 'B' and resid 528 through 543 Processing helix chain 'B' and resid 560 through 576 removed outlier: 3.656A pdb=" N ILE B 564 " --> pdb=" O ASN B 560 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG B 569 " --> pdb=" O GLU B 565 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU B 576 " --> pdb=" O ALA B 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 82 Processing helix chain 'C' and resid 157 through 162 removed outlier: 3.616A pdb=" N PHE C 162 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 177 Processing helix chain 'C' and resid 202 through 222 removed outlier: 3.546A pdb=" N LEU C 221 " --> pdb=" O CYS C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 237 removed outlier: 4.245A pdb=" N LYS C 236 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY C 237 " --> pdb=" O ALA C 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 232 through 237' Processing helix chain 'C' and resid 342 through 354 removed outlier: 3.546A pdb=" N PHE C 354 " --> pdb=" O LEU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 364 removed outlier: 3.866A pdb=" N ALA C 361 " --> pdb=" O HIS C 358 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N TRP C 362 " --> pdb=" O GLY C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 386 removed outlier: 4.031A pdb=" N ALA C 381 " --> pdb=" O ASP C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 412 Processing helix chain 'C' and resid 428 through 439 removed outlier: 4.804A pdb=" N LEU C 434 " --> pdb=" O GLN C 430 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN C 435 " --> pdb=" O MET C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 457 Processing helix chain 'C' and resid 462 through 467 removed outlier: 3.983A pdb=" N PHE C 466 " --> pdb=" O GLY C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 499 removed outlier: 3.614A pdb=" N LEU C 499 " --> pdb=" O ARG C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 509 Processing helix chain 'C' and resid 514 through 523 Processing helix chain 'C' and resid 528 through 544 removed outlier: 3.684A pdb=" N ARG C 532 " --> pdb=" O HIS C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 575 removed outlier: 3.753A pdb=" N ILE C 564 " --> pdb=" O ASN C 560 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU C 565 " --> pdb=" O ALA C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 601 removed outlier: 3.618A pdb=" N ASN C 601 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 92 through 93 Processing sheet with id=AA2, first strand: chain 'E' and resid 92 through 93 removed outlier: 9.018A pdb=" N PHE E 191 " --> pdb=" O VAL E 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 139 through 145 Processing sheet with id=AA4, first strand: chain 'E' and resid 248 through 249 removed outlier: 6.858A pdb=" N ILE E 266 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA E 294 " --> pdb=" O ILE E 266 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL E 268 " --> pdb=" O GLN E 292 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN E 292 " --> pdb=" O VAL E 268 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR E 270 " --> pdb=" O LEU E 290 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA E 294 " --> pdb=" O THR E 330 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASP E 331 " --> pdb=" O ASP E 421 " (cutoff:3.500A) removed outlier: 11.019A pdb=" N ASN E 423 " --> pdb=" O ASP E 331 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N PHE E 418 " --> pdb=" O TYR E 559 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TYR E 550 " --> pdb=" O ASN E 486 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASN E 486 " --> pdb=" O TYR E 550 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY E 552 " --> pdb=" O LEU E 484 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 475 through 476 removed outlier: 5.175A pdb=" N PHE E 418 " --> pdb=" O TYR E 559 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASP E 331 " --> pdb=" O ASP E 421 " (cutoff:3.500A) removed outlier: 11.019A pdb=" N ASN E 423 " --> pdb=" O ASP E 331 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA E 294 " --> pdb=" O THR E 330 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR E 270 " --> pdb=" O LEU E 290 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN E 292 " --> pdb=" O VAL E 268 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL E 268 " --> pdb=" O GLN E 292 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA E 294 " --> pdb=" O ILE E 266 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE E 266 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU E 243 " --> pdb=" O THR E 579 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 254 through 255 Processing sheet with id=AA7, first strand: chain 'A' and resid 92 through 96 Processing sheet with id=AA8, first strand: chain 'A' and resid 92 through 96 removed outlier: 4.116A pdb=" N SER A 106 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 127 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE A 191 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 242 through 249 removed outlier: 4.244A pdb=" N THR A 242 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG A 272 " --> pdb=" O LYS A 289 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LYS A 289 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA A 294 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N TRP A 323 " --> pdb=" O ASN A 415 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N VAL A 417 " --> pdb=" O TRP A 323 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA A 325 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N GLN A 419 " --> pdb=" O ALA A 325 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL A 327 " --> pdb=" O GLN A 419 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ASP A 421 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ILE A 329 " --> pdb=" O ASP A 421 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ASN A 423 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 11.407A pdb=" N ASP A 331 " --> pdb=" O ASN A 423 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE A 418 " --> pdb=" O TYR A 559 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 242 through 249 removed outlier: 4.244A pdb=" N THR A 242 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG A 272 " --> pdb=" O LYS A 289 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LYS A 289 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA A 294 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N TRP A 323 " --> pdb=" O ASN A 415 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N VAL A 417 " --> pdb=" O TRP A 323 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA A 325 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N GLN A 419 " --> pdb=" O ALA A 325 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL A 327 " --> pdb=" O GLN A 419 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ASP A 421 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ILE A 329 " --> pdb=" O ASP A 421 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ASN A 423 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 11.407A pdb=" N ASP A 331 " --> pdb=" O ASN A 423 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE A 418 " --> pdb=" O TYR A 559 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU A 484 " --> pdb=" O THR A 551 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 254 through 255 Processing sheet with id=AB3, first strand: chain 'B' and resid 92 through 93 Processing sheet with id=AB4, first strand: chain 'B' and resid 92 through 93 removed outlier: 9.018A pdb=" N PHE B 191 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 139 through 145 Processing sheet with id=AB6, first strand: chain 'B' and resid 248 through 249 removed outlier: 6.858A pdb=" N ILE B 266 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA B 294 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL B 268 " --> pdb=" O GLN B 292 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN B 292 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR B 270 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA B 294 " --> pdb=" O THR B 330 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASP B 331 " --> pdb=" O ASP B 421 " (cutoff:3.500A) removed outlier: 11.019A pdb=" N ASN B 423 " --> pdb=" O ASP B 331 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N PHE B 418 " --> pdb=" O TYR B 559 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TYR B 550 " --> pdb=" O ASN B 486 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASN B 486 " --> pdb=" O TYR B 550 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY B 552 " --> pdb=" O LEU B 484 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 475 through 476 removed outlier: 5.175A pdb=" N PHE B 418 " --> pdb=" O TYR B 559 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASP B 331 " --> pdb=" O ASP B 421 " (cutoff:3.500A) removed outlier: 11.019A pdb=" N ASN B 423 " --> pdb=" O ASP B 331 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA B 294 " --> pdb=" O THR B 330 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR B 270 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN B 292 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL B 268 " --> pdb=" O GLN B 292 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA B 294 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE B 266 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU B 243 " --> pdb=" O THR B 579 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 254 through 255 Processing sheet with id=AB9, first strand: chain 'C' and resid 92 through 96 Processing sheet with id=AC1, first strand: chain 'C' and resid 92 through 96 removed outlier: 4.116A pdb=" N SER C 106 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C 127 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE C 191 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 242 through 249 removed outlier: 4.244A pdb=" N THR C 242 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG C 272 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LYS C 289 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA C 294 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N TRP C 323 " --> pdb=" O ASN C 415 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N VAL C 417 " --> pdb=" O TRP C 323 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA C 325 " --> pdb=" O VAL C 417 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N GLN C 419 " --> pdb=" O ALA C 325 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL C 327 " --> pdb=" O GLN C 419 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ASP C 421 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ILE C 329 " --> pdb=" O ASP C 421 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ASN C 423 " --> pdb=" O ILE C 329 " (cutoff:3.500A) removed outlier: 11.407A pdb=" N ASP C 331 " --> pdb=" O ASN C 423 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE C 418 " --> pdb=" O TYR C 559 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 242 through 249 removed outlier: 4.244A pdb=" N THR C 242 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG C 272 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LYS C 289 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA C 294 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N TRP C 323 " --> pdb=" O ASN C 415 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N VAL C 417 " --> pdb=" O TRP C 323 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA C 325 " --> pdb=" O VAL C 417 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N GLN C 419 " --> pdb=" O ALA C 325 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL C 327 " --> pdb=" O GLN C 419 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ASP C 421 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ILE C 329 " --> pdb=" O ASP C 421 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ASN C 423 " --> pdb=" O ILE C 329 " (cutoff:3.500A) removed outlier: 11.407A pdb=" N ASP C 331 " --> pdb=" O ASN C 423 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE C 418 " --> pdb=" O TYR C 559 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU C 484 " --> pdb=" O THR C 551 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 254 through 255 814 hydrogen bonds defined for protein. 2184 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: 5.44 Time building geometry restraints manager: 4.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4776 1.33 - 1.45: 2534 1.45 - 1.57: 8892 1.57 - 1.70: 0 1.70 - 1.82: 92 Bond restraints: 16294 Sorted by residual: bond pdb=" N VAL A 412 " pdb=" CA VAL A 412 " ideal model delta sigma weight residual 1.458 1.500 -0.041 1.21e-02 6.83e+03 1.16e+01 bond pdb=" N VAL C 412 " pdb=" CA VAL C 412 " ideal model delta sigma weight residual 1.458 1.500 -0.041 1.21e-02 6.83e+03 1.16e+01 bond pdb=" N GLN C 411 " pdb=" CA GLN C 411 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.22e-02 6.72e+03 9.96e+00 bond pdb=" N GLN A 411 " pdb=" CA GLN A 411 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.22e-02 6.72e+03 9.96e+00 bond pdb=" N MET A 408 " pdb=" CA MET A 408 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.53e+00 ... (remaining 16289 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 21664 1.85 - 3.69: 362 3.69 - 5.54: 52 5.54 - 7.38: 20 7.38 - 9.23: 8 Bond angle restraints: 22106 Sorted by residual: angle pdb=" N GLN A 411 " pdb=" CA GLN A 411 " pdb=" C GLN A 411 " ideal model delta sigma weight residual 111.56 118.29 -6.73 1.53e+00 4.27e-01 1.93e+01 angle pdb=" N GLN C 411 " pdb=" CA GLN C 411 " pdb=" C GLN C 411 " ideal model delta sigma weight residual 111.56 118.29 -6.73 1.53e+00 4.27e-01 1.93e+01 angle pdb=" CA GLN C 411 " pdb=" C GLN C 411 " pdb=" O GLN C 411 " ideal model delta sigma weight residual 120.56 116.00 4.56 1.21e+00 6.83e-01 1.42e+01 angle pdb=" CA GLN A 411 " pdb=" C GLN A 411 " pdb=" O GLN A 411 " ideal model delta sigma weight residual 120.56 116.00 4.56 1.21e+00 6.83e-01 1.42e+01 angle pdb=" N GLN C 406 " pdb=" CA GLN C 406 " pdb=" C GLN C 406 " ideal model delta sigma weight residual 111.03 107.03 4.00 1.11e+00 8.12e-01 1.30e+01 ... (remaining 22101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 8750 17.93 - 35.86: 852 35.86 - 53.79: 142 53.79 - 71.72: 32 71.72 - 89.65: 30 Dihedral angle restraints: 9806 sinusoidal: 3928 harmonic: 5878 Sorted by residual: dihedral pdb=" CB GLU E 573 " pdb=" CG GLU E 573 " pdb=" CD GLU E 573 " pdb=" OE1 GLU E 573 " ideal model delta sinusoidal sigma weight residual 0.00 -89.52 89.52 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU B 573 " pdb=" CG GLU B 573 " pdb=" CD GLU B 573 " pdb=" OE1 GLU B 573 " ideal model delta sinusoidal sigma weight residual 0.00 -89.52 89.52 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG B 76 " pdb=" CD ARG B 76 " pdb=" NE ARG B 76 " pdb=" CZ ARG B 76 " ideal model delta sinusoidal sigma weight residual -90.00 -134.44 44.44 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 9803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1816 0.040 - 0.081: 426 0.081 - 0.121: 176 0.121 - 0.161: 24 0.161 - 0.202: 10 Chirality restraints: 2452 Sorted by residual: chirality pdb=" CA GLN C 406 " pdb=" N GLN C 406 " pdb=" C GLN C 406 " pdb=" CB GLN C 406 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA GLN A 406 " pdb=" N GLN A 406 " pdb=" C GLN A 406 " pdb=" CB GLN A 406 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA GLN A 411 " pdb=" N GLN A 411 " pdb=" C GLN A 411 " pdb=" CB GLN A 411 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.20 2.00e-01 2.50e+01 9.52e-01 ... (remaining 2449 not shown) Planarity restraints: 2970 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 405 " 0.022 2.00e-02 2.50e+03 4.51e-02 2.04e+01 pdb=" C GLY A 405 " -0.078 2.00e-02 2.50e+03 pdb=" O GLY A 405 " 0.030 2.00e-02 2.50e+03 pdb=" N GLN A 406 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 405 " -0.022 2.00e-02 2.50e+03 4.51e-02 2.04e+01 pdb=" C GLY C 405 " 0.078 2.00e-02 2.50e+03 pdb=" O GLY C 405 " -0.030 2.00e-02 2.50e+03 pdb=" N GLN C 406 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 367 " -0.028 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO E 368 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO E 368 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 368 " -0.024 5.00e-02 4.00e+02 ... (remaining 2967 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 440 2.70 - 3.25: 16556 3.25 - 3.80: 24249 3.80 - 4.35: 30313 4.35 - 4.90: 49078 Nonbonded interactions: 120636 Sorted by model distance: nonbonded pdb=" O ASP B 581 " pdb=" OD1 ASN B 582 " model vdw 2.146 3.040 nonbonded pdb=" O ASP E 581 " pdb=" OD1 ASN E 582 " model vdw 2.146 3.040 nonbonded pdb=" OG1 THR A 270 " pdb=" OD1 ASN A 291 " model vdw 2.195 3.040 nonbonded pdb=" OG1 THR C 270 " pdb=" OD1 ASN C 291 " model vdw 2.195 3.040 nonbonded pdb=" OD1 ASN A 595 " pdb=" OH TYR B 519 " model vdw 2.209 3.040 ... (remaining 120631 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 63 through 273 or resid 287 through 369 or (resid 370 and \ (name N or name CA or name C or name O or name CB )) or resid 371 through 582)) selection = (chain 'B' and (resid 63 through 137 or resid 155 through 303 or resid 320 throu \ gh 582)) selection = (chain 'C' and (resid 63 through 273 or resid 287 through 369 or (resid 370 and \ (name N or name CA or name C or name O or name CB )) or resid 371 through 582)) selection = (chain 'E' and (resid 63 through 137 or resid 155 through 303 or resid 320 throu \ gh 582)) } 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 41.140 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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 0.041 16294 Z= 0.164 Angle : 0.611 9.230 22106 Z= 0.319 Chirality : 0.043 0.202 2452 Planarity : 0.003 0.045 2970 Dihedral : 15.139 89.654 6006 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 2026 helix: 1.05 (0.20), residues: 714 sheet: -0.24 (0.27), residues: 392 loop : -0.79 (0.22), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 487 HIS 0.002 0.001 HIS C 101 PHE 0.018 0.001 PHE C 404 TYR 0.014 0.001 TYR C 570 ARG 0.005 0.000 ARG A 541 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 354 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 129 LEU cc_start: 0.9502 (mp) cc_final: 0.9247 (mt) REVERT: E 436 LEU cc_start: 0.8781 (mp) cc_final: 0.8565 (mt) REVERT: E 505 LEU cc_start: 0.8814 (tp) cc_final: 0.8497 (tp) REVERT: A 256 ASP cc_start: 0.7632 (p0) cc_final: 0.7379 (p0) REVERT: A 432 ASP cc_start: 0.7885 (m-30) cc_final: 0.7354 (m-30) REVERT: B 129 LEU cc_start: 0.9502 (mp) cc_final: 0.9246 (mt) REVERT: B 436 LEU cc_start: 0.8779 (mp) cc_final: 0.8565 (mt) REVERT: B 505 LEU cc_start: 0.8814 (tp) cc_final: 0.8499 (tp) REVERT: C 256 ASP cc_start: 0.7634 (p0) cc_final: 0.7381 (p0) REVERT: C 432 ASP cc_start: 0.7881 (m-30) cc_final: 0.7350 (m-30) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.2343 time to fit residues: 127.7335 Evaluate side-chains 272 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.6980 chunk 154 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 159 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 313 ASN A 411 GLN A 413 GLN B 313 ASN B 533 ASN C 411 GLN C 413 GLN C 445 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16294 Z= 0.230 Angle : 0.579 8.145 22106 Z= 0.293 Chirality : 0.043 0.172 2452 Planarity : 0.004 0.043 2970 Dihedral : 3.819 14.292 2208 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.91 % Favored : 92.99 % Rotamer: Outliers : 0.12 % Allowed : 6.26 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 2026 helix: 1.06 (0.20), residues: 732 sheet: -0.40 (0.27), residues: 402 loop : -0.73 (0.23), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 487 HIS 0.003 0.001 HIS C 255 PHE 0.012 0.001 PHE C 167 TYR 0.015 0.001 TYR B 559 ARG 0.005 0.000 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 326 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 295 MET cc_start: 0.8031 (ptt) cc_final: 0.7780 (ptt) REVERT: E 384 TRP cc_start: 0.8353 (m100) cc_final: 0.7657 (m100) REVERT: E 505 LEU cc_start: 0.8876 (tp) cc_final: 0.8538 (tp) REVERT: A 256 ASP cc_start: 0.7698 (p0) cc_final: 0.7343 (p0) REVERT: A 408 MET cc_start: 0.9092 (tpp) cc_final: 0.8305 (tpp) REVERT: A 432 ASP cc_start: 0.7962 (m-30) cc_final: 0.7510 (m-30) REVERT: B 295 MET cc_start: 0.8029 (ptt) cc_final: 0.7777 (ptt) REVERT: B 384 TRP cc_start: 0.8353 (m100) cc_final: 0.7658 (m100) REVERT: B 505 LEU cc_start: 0.8876 (tp) cc_final: 0.8539 (tp) REVERT: C 256 ASP cc_start: 0.7694 (p0) cc_final: 0.7338 (p0) REVERT: C 408 MET cc_start: 0.9092 (tpp) cc_final: 0.8305 (tpp) REVERT: C 432 ASP cc_start: 0.7959 (m-30) cc_final: 0.7509 (m-30) outliers start: 2 outliers final: 0 residues processed: 326 average time/residue: 0.2408 time to fit residues: 120.5820 Evaluate side-chains 264 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 185 optimal weight: 0.5980 chunk 200 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 148 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16294 Z= 0.153 Angle : 0.553 8.879 22106 Z= 0.275 Chirality : 0.042 0.161 2452 Planarity : 0.003 0.042 2970 Dihedral : 3.744 13.399 2208 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.61 % Favored : 93.29 % Rotamer: Outliers : 0.06 % Allowed : 4.37 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.20), residues: 2026 helix: 1.14 (0.20), residues: 732 sheet: -0.33 (0.26), residues: 406 loop : -0.74 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 487 HIS 0.002 0.000 HIS E 101 PHE 0.009 0.001 PHE C 167 TYR 0.020 0.001 TYR A 570 ARG 0.003 0.000 ARG E 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 346 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 384 TRP cc_start: 0.8289 (m100) cc_final: 0.7597 (m100) REVERT: E 505 LEU cc_start: 0.8827 (tp) cc_final: 0.8448 (tp) REVERT: A 218 ASP cc_start: 0.7827 (t70) cc_final: 0.7487 (t0) REVERT: A 256 ASP cc_start: 0.7666 (p0) cc_final: 0.7243 (p0) REVERT: A 408 MET cc_start: 0.9152 (tpp) cc_final: 0.8430 (tpp) REVERT: A 412 VAL cc_start: 0.9239 (t) cc_final: 0.8956 (m) REVERT: A 432 ASP cc_start: 0.8146 (m-30) cc_final: 0.7809 (m-30) REVERT: A 492 GLU cc_start: 0.7504 (pm20) cc_final: 0.6652 (pm20) REVERT: B 384 TRP cc_start: 0.8289 (m100) cc_final: 0.7598 (m100) REVERT: B 505 LEU cc_start: 0.8828 (tp) cc_final: 0.8450 (tp) REVERT: C 218 ASP cc_start: 0.7832 (t70) cc_final: 0.7489 (t0) REVERT: C 256 ASP cc_start: 0.7662 (p0) cc_final: 0.7237 (p0) REVERT: C 408 MET cc_start: 0.9150 (tpp) cc_final: 0.8425 (tpp) REVERT: C 412 VAL cc_start: 0.9240 (t) cc_final: 0.8956 (m) REVERT: C 432 ASP cc_start: 0.8143 (m-30) cc_final: 0.7809 (m-30) REVERT: C 492 GLU cc_start: 0.7506 (pm20) cc_final: 0.6653 (pm20) outliers start: 1 outliers final: 0 residues processed: 346 average time/residue: 0.2414 time to fit residues: 128.8521 Evaluate side-chains 264 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 88 optimal weight: 0.0570 chunk 124 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 overall best weight: 1.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 314 GLN A 117 ASN A 119 GLN ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN C 117 ASN ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16294 Z= 0.203 Angle : 0.571 8.493 22106 Z= 0.286 Chirality : 0.043 0.175 2452 Planarity : 0.004 0.041 2970 Dihedral : 3.834 14.068 2208 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.20), residues: 2026 helix: 1.08 (0.20), residues: 732 sheet: -0.37 (0.26), residues: 402 loop : -0.75 (0.23), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 487 HIS 0.002 0.001 HIS B 101 PHE 0.013 0.001 PHE C 283 TYR 0.012 0.001 TYR A 543 ARG 0.003 0.000 ARG C 497 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 384 TRP cc_start: 0.8366 (m100) cc_final: 0.7638 (m100) REVERT: E 425 MET cc_start: 0.8622 (tpp) cc_final: 0.7775 (mpp) REVERT: E 505 LEU cc_start: 0.8779 (tp) cc_final: 0.8251 (tp) REVERT: A 215 ASN cc_start: 0.8609 (t0) cc_final: 0.8406 (t0) REVERT: A 256 ASP cc_start: 0.7613 (p0) cc_final: 0.7206 (p0) REVERT: A 408 MET cc_start: 0.9262 (tpp) cc_final: 0.8550 (tpp) REVERT: A 412 VAL cc_start: 0.9317 (t) cc_final: 0.9043 (m) REVERT: A 432 ASP cc_start: 0.8205 (m-30) cc_final: 0.7846 (m-30) REVERT: A 492 GLU cc_start: 0.7523 (pm20) cc_final: 0.6514 (pm20) REVERT: B 384 TRP cc_start: 0.8366 (m100) cc_final: 0.7638 (m100) REVERT: B 425 MET cc_start: 0.8623 (tpp) cc_final: 0.7778 (mpp) REVERT: B 505 LEU cc_start: 0.8781 (tp) cc_final: 0.8253 (tp) REVERT: C 215 ASN cc_start: 0.8609 (t0) cc_final: 0.8408 (t0) REVERT: C 256 ASP cc_start: 0.7619 (p0) cc_final: 0.7209 (p0) REVERT: C 408 MET cc_start: 0.9259 (tpp) cc_final: 0.8551 (tpp) REVERT: C 412 VAL cc_start: 0.9316 (t) cc_final: 0.9042 (m) REVERT: C 432 ASP cc_start: 0.8207 (m-30) cc_final: 0.7850 (m-30) REVERT: C 492 GLU cc_start: 0.7523 (pm20) cc_final: 0.6516 (pm20) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.2360 time to fit residues: 118.6491 Evaluate side-chains 268 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 136 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 0.3980 chunk 176 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 533 ASN A 119 GLN A 279 GLN ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 GLN C 472 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16294 Z= 0.227 Angle : 0.579 8.482 22106 Z= 0.292 Chirality : 0.043 0.179 2452 Planarity : 0.004 0.040 2970 Dihedral : 3.915 15.454 2208 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.12 % Allowed : 4.08 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.20), residues: 2026 helix: 1.05 (0.20), residues: 732 sheet: -0.37 (0.26), residues: 402 loop : -0.82 (0.23), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 487 HIS 0.003 0.001 HIS B 101 PHE 0.013 0.001 PHE B 296 TYR 0.020 0.002 TYR A 570 ARG 0.003 0.000 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 320 time to evaluate : 1.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 384 TRP cc_start: 0.8343 (m100) cc_final: 0.7656 (m100) REVERT: E 505 LEU cc_start: 0.8754 (tp) cc_final: 0.8411 (tp) REVERT: A 256 ASP cc_start: 0.7644 (p0) cc_final: 0.7235 (p0) REVERT: A 408 MET cc_start: 0.9261 (tpp) cc_final: 0.8519 (tpp) REVERT: A 412 VAL cc_start: 0.9352 (t) cc_final: 0.9085 (m) REVERT: A 432 ASP cc_start: 0.7840 (m-30) cc_final: 0.7365 (m-30) REVERT: A 492 GLU cc_start: 0.7572 (pm20) cc_final: 0.6675 (pm20) REVERT: B 384 TRP cc_start: 0.8342 (m100) cc_final: 0.7657 (m100) REVERT: B 505 LEU cc_start: 0.8751 (tp) cc_final: 0.8408 (tp) REVERT: C 256 ASP cc_start: 0.7645 (p0) cc_final: 0.7237 (p0) REVERT: C 408 MET cc_start: 0.9261 (tpp) cc_final: 0.8525 (tpp) REVERT: C 412 VAL cc_start: 0.9353 (t) cc_final: 0.9084 (m) REVERT: C 432 ASP cc_start: 0.7843 (m-30) cc_final: 0.7369 (m-30) REVERT: C 492 GLU cc_start: 0.7573 (pm20) cc_final: 0.6677 (pm20) outliers start: 2 outliers final: 0 residues processed: 322 average time/residue: 0.2555 time to fit residues: 126.6205 Evaluate side-chains 272 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 0.2980 chunk 177 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 197 optimal weight: 4.9990 chunk 163 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 65 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN C 445 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16294 Z= 0.285 Angle : 0.621 8.650 22106 Z= 0.316 Chirality : 0.045 0.163 2452 Planarity : 0.004 0.040 2970 Dihedral : 4.123 15.374 2208 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.19), residues: 2026 helix: 0.93 (0.20), residues: 730 sheet: -0.46 (0.26), residues: 392 loop : -0.94 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 105 HIS 0.003 0.001 HIS B 101 PHE 0.016 0.001 PHE B 296 TYR 0.022 0.002 TYR A 559 ARG 0.003 0.000 ARG E 497 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 1.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 384 TRP cc_start: 0.8397 (m100) cc_final: 0.7679 (m100) REVERT: E 505 LEU cc_start: 0.8757 (tp) cc_final: 0.8396 (tp) REVERT: A 256 ASP cc_start: 0.7750 (p0) cc_final: 0.7326 (p0) REVERT: A 408 MET cc_start: 0.9246 (tpp) cc_final: 0.8541 (tpp) REVERT: A 412 VAL cc_start: 0.9376 (t) cc_final: 0.9130 (m) REVERT: A 432 ASP cc_start: 0.7982 (m-30) cc_final: 0.7754 (m-30) REVERT: B 384 TRP cc_start: 0.8397 (m100) cc_final: 0.7679 (m100) REVERT: B 505 LEU cc_start: 0.8755 (tp) cc_final: 0.8395 (tp) REVERT: C 256 ASP cc_start: 0.7750 (p0) cc_final: 0.7327 (p0) REVERT: C 408 MET cc_start: 0.9245 (tpp) cc_final: 0.8543 (tpp) REVERT: C 412 VAL cc_start: 0.9376 (t) cc_final: 0.9128 (m) REVERT: C 432 ASP cc_start: 0.7979 (m-30) cc_final: 0.7752 (m-30) outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.2460 time to fit residues: 118.9539 Evaluate side-chains 274 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 144 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 196 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16294 Z= 0.151 Angle : 0.576 8.247 22106 Z= 0.286 Chirality : 0.043 0.162 2452 Planarity : 0.003 0.040 2970 Dihedral : 3.833 15.662 2208 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.06 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.20), residues: 2026 helix: 1.10 (0.20), residues: 730 sheet: -0.21 (0.27), residues: 394 loop : -0.83 (0.23), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 384 HIS 0.002 0.000 HIS A 101 PHE 0.011 0.001 PHE E 296 TYR 0.011 0.001 TYR C 543 ARG 0.002 0.000 ARG B 497 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 505 LEU cc_start: 0.8745 (tp) cc_final: 0.8398 (tp) REVERT: A 256 ASP cc_start: 0.7626 (p0) cc_final: 0.7145 (p0) REVERT: A 408 MET cc_start: 0.9214 (tpp) cc_final: 0.8382 (tpp) REVERT: A 412 VAL cc_start: 0.9341 (t) cc_final: 0.9065 (m) REVERT: A 432 ASP cc_start: 0.7966 (m-30) cc_final: 0.7690 (m-30) REVERT: B 505 LEU cc_start: 0.8746 (tp) cc_final: 0.8399 (tp) REVERT: C 256 ASP cc_start: 0.7626 (p0) cc_final: 0.7147 (p0) REVERT: C 408 MET cc_start: 0.9212 (tpp) cc_final: 0.8387 (tpp) REVERT: C 412 VAL cc_start: 0.9340 (t) cc_final: 0.9067 (m) REVERT: C 432 ASP cc_start: 0.7968 (m-30) cc_final: 0.7688 (m-30) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.2401 time to fit residues: 125.1939 Evaluate side-chains 277 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 chunk 178 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16294 Z= 0.253 Angle : 0.619 9.003 22106 Z= 0.309 Chirality : 0.044 0.161 2452 Planarity : 0.004 0.040 2970 Dihedral : 4.012 14.181 2208 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.00 % Favored : 91.91 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.19), residues: 2026 helix: 0.99 (0.20), residues: 732 sheet: -0.28 (0.27), residues: 382 loop : -0.96 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 487 HIS 0.003 0.001 HIS E 101 PHE 0.015 0.001 PHE B 296 TYR 0.017 0.002 TYR E 559 ARG 0.003 0.000 ARG E 497 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 384 TRP cc_start: 0.8392 (m100) cc_final: 0.7666 (m100) REVERT: E 505 LEU cc_start: 0.8746 (tp) cc_final: 0.8374 (tp) REVERT: A 84 GLN cc_start: 0.7789 (tp40) cc_final: 0.7578 (tp40) REVERT: A 256 ASP cc_start: 0.7648 (p0) cc_final: 0.7229 (p0) REVERT: A 408 MET cc_start: 0.9231 (tpp) cc_final: 0.8503 (tpp) REVERT: A 412 VAL cc_start: 0.9394 (t) cc_final: 0.9173 (m) REVERT: A 432 ASP cc_start: 0.8060 (m-30) cc_final: 0.7786 (m-30) REVERT: B 384 TRP cc_start: 0.8388 (m100) cc_final: 0.7662 (m100) REVERT: B 505 LEU cc_start: 0.8747 (tp) cc_final: 0.8376 (tp) REVERT: C 84 GLN cc_start: 0.7794 (tp40) cc_final: 0.7583 (tp40) REVERT: C 256 ASP cc_start: 0.7650 (p0) cc_final: 0.7232 (p0) REVERT: C 408 MET cc_start: 0.9230 (tpp) cc_final: 0.8505 (tpp) REVERT: C 412 VAL cc_start: 0.9393 (t) cc_final: 0.9174 (m) REVERT: C 432 ASP cc_start: 0.8059 (m-30) cc_final: 0.7784 (m-30) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.2395 time to fit residues: 118.2330 Evaluate side-chains 280 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 0.0980 chunk 171 optimal weight: 0.8980 chunk 183 optimal weight: 0.8980 chunk 110 optimal weight: 0.2980 chunk 79 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 165 optimal weight: 0.7980 chunk 173 optimal weight: 0.0870 chunk 182 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16294 Z= 0.143 Angle : 0.587 9.281 22106 Z= 0.292 Chirality : 0.043 0.171 2452 Planarity : 0.004 0.041 2970 Dihedral : 3.752 15.702 2208 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.86 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.20), residues: 2026 helix: 1.06 (0.20), residues: 732 sheet: -0.16 (0.27), residues: 394 loop : -0.84 (0.23), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 347 HIS 0.002 0.000 HIS C 101 PHE 0.010 0.001 PHE C 283 TYR 0.015 0.002 TYR B 166 ARG 0.007 0.000 ARG E 56 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 425 MET cc_start: 0.8653 (tpp) cc_final: 0.7796 (mpp) REVERT: E 505 LEU cc_start: 0.8820 (tp) cc_final: 0.8449 (tp) REVERT: A 84 GLN cc_start: 0.7654 (tp40) cc_final: 0.7447 (tp40) REVERT: A 256 ASP cc_start: 0.7657 (p0) cc_final: 0.7162 (p0) REVERT: A 408 MET cc_start: 0.9169 (tpp) cc_final: 0.8272 (tpp) REVERT: A 412 VAL cc_start: 0.9331 (t) cc_final: 0.9105 (m) REVERT: A 432 ASP cc_start: 0.7771 (m-30) cc_final: 0.7517 (m-30) REVERT: A 492 GLU cc_start: 0.7360 (pm20) cc_final: 0.6487 (pm20) REVERT: B 425 MET cc_start: 0.8655 (tpp) cc_final: 0.7784 (mpp) REVERT: B 505 LEU cc_start: 0.8823 (tp) cc_final: 0.8452 (tp) REVERT: C 84 GLN cc_start: 0.7654 (tp40) cc_final: 0.7446 (tp40) REVERT: C 256 ASP cc_start: 0.7559 (p0) cc_final: 0.7110 (p0) REVERT: C 408 MET cc_start: 0.9169 (tpp) cc_final: 0.8275 (tpp) REVERT: C 412 VAL cc_start: 0.9332 (t) cc_final: 0.9106 (m) REVERT: C 432 ASP cc_start: 0.7778 (m-30) cc_final: 0.7521 (m-30) REVERT: C 492 GLU cc_start: 0.7355 (pm20) cc_final: 0.6481 (pm20) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.2559 time to fit residues: 137.1615 Evaluate side-chains 283 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 134 optimal weight: 0.0270 chunk 203 optimal weight: 0.2980 chunk 187 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 125 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.6644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 271 GLN A 101 HIS ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN C 101 HIS C 260 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16294 Z= 0.196 Angle : 0.593 9.191 22106 Z= 0.298 Chirality : 0.043 0.168 2452 Planarity : 0.004 0.041 2970 Dihedral : 3.827 14.353 2208 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.96 % Favored : 92.94 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.20), residues: 2026 helix: 1.05 (0.20), residues: 732 sheet: -0.22 (0.27), residues: 396 loop : -0.87 (0.23), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 487 HIS 0.003 0.001 HIS A 101 PHE 0.012 0.001 PHE A 283 TYR 0.017 0.002 TYR E 559 ARG 0.007 0.000 ARG B 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 384 TRP cc_start: 0.8348 (m100) cc_final: 0.7653 (m100) REVERT: E 425 MET cc_start: 0.8667 (tpp) cc_final: 0.7843 (tpp) REVERT: E 505 LEU cc_start: 0.8741 (tp) cc_final: 0.8359 (tp) REVERT: A 256 ASP cc_start: 0.7631 (p0) cc_final: 0.7104 (p0) REVERT: A 408 MET cc_start: 0.9220 (tpp) cc_final: 0.8401 (tpp) REVERT: A 412 VAL cc_start: 0.9368 (t) cc_final: 0.9155 (m) REVERT: A 432 ASP cc_start: 0.7801 (m-30) cc_final: 0.7446 (m-30) REVERT: A 492 GLU cc_start: 0.7361 (pm20) cc_final: 0.7135 (pm20) REVERT: B 384 TRP cc_start: 0.8352 (m100) cc_final: 0.7651 (m100) REVERT: B 425 MET cc_start: 0.8669 (tpp) cc_final: 0.7844 (tpp) REVERT: B 505 LEU cc_start: 0.8743 (tp) cc_final: 0.8362 (tp) REVERT: C 256 ASP cc_start: 0.7607 (p0) cc_final: 0.7152 (p0) REVERT: C 408 MET cc_start: 0.9220 (tpp) cc_final: 0.8404 (tpp) REVERT: C 412 VAL cc_start: 0.9370 (t) cc_final: 0.9160 (m) REVERT: C 432 ASP cc_start: 0.7807 (m-30) cc_final: 0.7459 (m-30) REVERT: C 492 GLU cc_start: 0.7358 (pm20) cc_final: 0.7132 (pm20) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.2364 time to fit residues: 119.2795 Evaluate side-chains 280 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 162 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 166 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 142 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.134734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.113352 restraints weight = 30280.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.116553 restraints weight = 18040.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.118800 restraints weight = 12545.441| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16294 Z= 0.156 Angle : 0.604 9.301 22106 Z= 0.299 Chirality : 0.043 0.170 2452 Planarity : 0.003 0.041 2970 Dihedral : 3.725 15.385 2208 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.96 % Favored : 92.94 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.20), residues: 2026 helix: 1.09 (0.20), residues: 732 sheet: -0.16 (0.27), residues: 398 loop : -0.86 (0.23), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 487 HIS 0.002 0.000 HIS B 101 PHE 0.012 0.001 PHE C 283 TYR 0.017 0.001 TYR E 559 ARG 0.005 0.000 ARG E 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3038.54 seconds wall clock time: 54 minutes 56.85 seconds (3296.85 seconds total)