Starting phenix.real_space_refine on Fri Aug 22 19:28:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w6h_37323/08_2025/8w6h_37323.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w6h_37323/08_2025/8w6h_37323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w6h_37323/08_2025/8w6h_37323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w6h_37323/08_2025/8w6h_37323.map" model { file = "/net/cci-nas-00/data/ceres_data/8w6h_37323/08_2025/8w6h_37323.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w6h_37323/08_2025/8w6h_37323.cif" } resolution = 3.1 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= -0.000 sd= 0.119 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 52 5.16 5 Na 2 4.78 5 C 4897 2.51 5 N 1098 2.21 5 O 1219 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7268 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3601 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 28, 'TRANS': 433} Chain breaks: 4 Chain: "B" Number of atoms: 3599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3599 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 27, 'TRANS': 433} Chain breaks: 4 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' NA': 1, 'CLR': 1, 'SO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' NA': 1, 'CLR': 1, 'SO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.06, per 1000 atoms: 0.28 Number of scatterers: 7268 At special positions: 0 Unit cell: (96.743, 84.786, 79.351, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 Na 2 11.00 O 1219 8.00 N 1098 7.00 C 4897 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: 0.61 Conformation dependent library (CDL) restraints added in 367.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1748 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 2 sheets defined 73.1% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 15 through 23 removed outlier: 3.979A pdb=" N LEU A 21 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 50 removed outlier: 3.519A pdb=" N CYS A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR A 46 " --> pdb=" O PHE A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 60 Processing helix chain 'A' and resid 61 through 70 Proline residue: A 67 - end of helix Processing helix chain 'A' and resid 83 through 102 removed outlier: 3.555A pdb=" N GLY A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER A 98 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 116 removed outlier: 3.785A pdb=" N VAL A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 134 removed outlier: 3.817A pdb=" N LEU A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE A 133 " --> pdb=" O SER A 129 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 160 removed outlier: 4.042A pdb=" N MET A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 147 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 236 through 251 removed outlier: 3.734A pdb=" N THR A 240 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.593A pdb=" N PHE A 265 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA A 266 " --> pdb=" O ASN A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 308 removed outlier: 3.517A pdb=" N PHE A 285 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) Proline residue: A 290 - end of helix removed outlier: 3.890A pdb=" N ILE A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.649A pdb=" N LYS A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 364 removed outlier: 3.989A pdb=" N ILE A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 394 removed outlier: 3.869A pdb=" N VAL A 388 " --> pdb=" O THR A 384 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 431 removed outlier: 3.503A pdb=" N SER A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 452 removed outlier: 3.863A pdb=" N ILE A 437 " --> pdb=" O TRP A 433 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 461 removed outlier: 3.746A pdb=" N LYS A 461 " --> pdb=" O TRP A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 removed outlier: 3.548A pdb=" N GLY A 466 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER A 467 " --> pdb=" O PRO A 464 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 468 " --> pdb=" O LEU A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 485 removed outlier: 3.542A pdb=" N ILE A 473 " --> pdb=" O PRO A 469 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET A 480 " --> pdb=" O ILE A 476 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 508 removed outlier: 3.664A pdb=" N PHE A 497 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 498 " --> pdb=" O ILE A 494 " (cutoff:3.500A) Proline residue: A 499 - end of helix removed outlier: 3.524A pdb=" N SER A 502 " --> pdb=" O LEU A 498 " (cutoff:3.500A) Proline residue: A 503 - end of helix removed outlier: 3.600A pdb=" N GLU A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 521 Proline residue: A 518 - end of helix Processing helix chain 'A' and resid 534 through 539 removed outlier: 3.554A pdb=" N ILE A 538 " --> pdb=" O PRO A 534 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A 539 " --> pdb=" O PRO A 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 534 through 539' Processing helix chain 'A' and resid 540 through 542 No H-bonds generated for 'chain 'A' and resid 540 through 542' Processing helix chain 'A' and resid 547 through 572 removed outlier: 3.539A pdb=" N VAL A 551 " --> pdb=" O VAL A 547 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY A 556 " --> pdb=" O LYS A 552 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 571 " --> pdb=" O LEU A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 578 Processing helix chain 'B' and resid 15 through 23 removed outlier: 3.979A pdb=" N LEU B 21 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 23 " --> pdb=" O THR B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 50 removed outlier: 3.518A pdb=" N CYS B 37 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR B 46 " --> pdb=" O PHE B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 60 Processing helix chain 'B' and resid 61 through 70 Proline residue: B 67 - end of helix Processing helix chain 'B' and resid 83 through 102 removed outlier: 3.554A pdb=" N GLY B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER B 98 " --> pdb=" O CYS B 94 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 removed outlier: 3.785A pdb=" N VAL B 113 " --> pdb=" O ALA B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 134 removed outlier: 3.816A pdb=" N LEU B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE B 133 " --> pdb=" O SER B 129 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU B 134 " --> pdb=" O SER B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 160 removed outlier: 4.042A pdb=" N MET B 146 " --> pdb=" O SER B 142 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL B 147 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Proline residue: B 149 - end of helix Processing helix chain 'B' and resid 236 through 251 removed outlier: 3.733A pdb=" N THR B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU B 242 " --> pdb=" O LYS B 238 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 271 removed outlier: 3.593A pdb=" N PHE B 265 " --> pdb=" O THR B 261 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 266 " --> pdb=" O ASN B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 308 removed outlier: 3.518A pdb=" N PHE B 285 " --> pdb=" O PHE B 281 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) Proline residue: B 290 - end of helix removed outlier: 3.890A pdb=" N ILE B 294 " --> pdb=" O PRO B 290 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.650A pdb=" N LYS B 339 " --> pdb=" O GLN B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 364 removed outlier: 3.988A pdb=" N ILE B 348 " --> pdb=" O ARG B 344 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 350 " --> pdb=" O GLN B 346 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 394 removed outlier: 3.869A pdb=" N VAL B 388 " --> pdb=" O THR B 384 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 390 " --> pdb=" O SER B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 431 removed outlier: 3.502A pdb=" N SER B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 452 removed outlier: 3.862A pdb=" N ILE B 437 " --> pdb=" O TRP B 433 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER B 452 " --> pdb=" O GLY B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 461 removed outlier: 3.746A pdb=" N LYS B 461 " --> pdb=" O TRP B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 removed outlier: 3.549A pdb=" N GLY B 466 " --> pdb=" O SER B 463 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER B 467 " --> pdb=" O PRO B 464 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU B 468 " --> pdb=" O LEU B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 485 removed outlier: 3.542A pdb=" N ILE B 473 " --> pdb=" O PRO B 469 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET B 480 " --> pdb=" O ILE B 476 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 508 removed outlier: 3.665A pdb=" N PHE B 497 " --> pdb=" O THR B 493 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 498 " --> pdb=" O ILE B 494 " (cutoff:3.500A) Proline residue: B 499 - end of helix removed outlier: 3.524A pdb=" N SER B 502 " --> pdb=" O LEU B 498 " (cutoff:3.500A) Proline residue: B 503 - end of helix removed outlier: 3.601A pdb=" N GLU B 506 " --> pdb=" O SER B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 521 Proline residue: B 518 - end of helix Processing helix chain 'B' and resid 534 through 539 removed outlier: 3.554A pdb=" N ILE B 538 " --> pdb=" O PRO B 534 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL B 539 " --> pdb=" O PRO B 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 534 through 539' Processing helix chain 'B' and resid 540 through 542 No H-bonds generated for 'chain 'B' and resid 540 through 542' Processing helix chain 'B' and resid 546 through 572 removed outlier: 3.921A pdb=" N MET B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 551 " --> pdb=" O VAL B 547 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY B 556 " --> pdb=" O LYS B 552 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS B 570 " --> pdb=" O MET B 566 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 571 " --> pdb=" O LEU B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 578 Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.792A pdb=" N SER A 419 " --> pdb=" O ALA A 401 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 400 through 402 removed outlier: 6.793A pdb=" N SER B 419 " --> pdb=" O ALA B 401 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 978 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: 0.98 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1049 1.29 - 1.42: 1957 1.42 - 1.55: 4385 1.55 - 1.68: 2 1.68 - 1.81: 82 Bond restraints: 7475 Sorted by residual: bond pdb=" C16 CLR B 603 " pdb=" C17 CLR B 603 " ideal model delta sigma weight residual 1.554 1.442 0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" C16 CLR A 603 " pdb=" C17 CLR A 603 " ideal model delta sigma weight residual 1.554 1.442 0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" C13 CLR B 603 " pdb=" C14 CLR B 603 " ideal model delta sigma weight residual 1.537 1.426 0.111 2.00e-02 2.50e+03 3.09e+01 bond pdb=" C13 CLR A 603 " pdb=" C14 CLR A 603 " ideal model delta sigma weight residual 1.537 1.427 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C THR B 259 " pdb=" O THR B 259 " ideal model delta sigma weight residual 1.233 1.162 0.071 1.30e-02 5.92e+03 2.95e+01 ... (remaining 7470 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 9822 2.61 - 5.21: 310 5.21 - 7.82: 72 7.82 - 10.43: 21 10.43 - 13.04: 10 Bond angle restraints: 10235 Sorted by residual: angle pdb=" C THR A 259 " pdb=" CA THR A 259 " pdb=" CB THR A 259 " ideal model delta sigma weight residual 110.45 118.40 -7.95 1.73e+00 3.34e-01 2.11e+01 angle pdb=" C THR B 259 " pdb=" CA THR B 259 " pdb=" CB THR B 259 " ideal model delta sigma weight residual 110.45 118.08 -7.63 1.73e+00 3.34e-01 1.95e+01 angle pdb=" C16 CLR B 603 " pdb=" C17 CLR B 603 " pdb=" C20 CLR B 603 " ideal model delta sigma weight residual 112.02 98.98 13.04 3.00e+00 1.11e-01 1.89e+01 angle pdb=" C16 CLR A 603 " pdb=" C17 CLR A 603 " pdb=" C20 CLR A 603 " ideal model delta sigma weight residual 112.02 99.01 13.01 3.00e+00 1.11e-01 1.88e+01 angle pdb=" N ASN B 119 " pdb=" CA ASN B 119 " pdb=" C ASN B 119 " ideal model delta sigma weight residual 111.53 120.92 -9.39 2.18e+00 2.10e-01 1.86e+01 ... (remaining 10230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 3874 15.99 - 31.99: 454 31.99 - 47.98: 82 47.98 - 63.97: 2 63.97 - 79.96: 10 Dihedral angle restraints: 4422 sinusoidal: 1735 harmonic: 2687 Sorted by residual: dihedral pdb=" CA ASN A 119 " pdb=" C ASN A 119 " pdb=" N PRO A 120 " pdb=" CA PRO A 120 " ideal model delta harmonic sigma weight residual 180.00 139.58 40.42 0 5.00e+00 4.00e-02 6.53e+01 dihedral pdb=" CA ASN B 119 " pdb=" C ASN B 119 " pdb=" N PRO B 120 " pdb=" CA PRO B 120 " ideal model delta harmonic sigma weight residual 180.00 139.58 40.42 0 5.00e+00 4.00e-02 6.53e+01 dihedral pdb=" CA PRO B 27 " pdb=" C PRO B 27 " pdb=" N ILE B 28 " pdb=" CA ILE B 28 " ideal model delta harmonic sigma weight residual 180.00 149.61 30.39 0 5.00e+00 4.00e-02 3.69e+01 ... (remaining 4419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1109 0.094 - 0.189: 125 0.189 - 0.283: 8 0.283 - 0.377: 6 0.377 - 0.471: 4 Chirality restraints: 1252 Sorted by residual: chirality pdb=" C10 CLR A 603 " pdb=" C1 CLR A 603 " pdb=" C5 CLR A 603 " pdb=" C9 CLR A 603 " both_signs ideal model delta sigma weight residual False -2.85 -2.38 -0.47 2.00e-01 2.50e+01 5.55e+00 chirality pdb=" C10 CLR B 603 " pdb=" C1 CLR B 603 " pdb=" C5 CLR B 603 " pdb=" C9 CLR B 603 " both_signs ideal model delta sigma weight residual False -2.85 -2.38 -0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" CA ASN B 119 " pdb=" N ASN B 119 " pdb=" C ASN B 119 " pdb=" CB ASN B 119 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.39 2.00e-01 2.50e+01 3.71e+00 ... (remaining 1249 not shown) Planarity restraints: 1195 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 534 " 0.074 5.00e-02 4.00e+02 1.10e-01 1.92e+01 pdb=" N PRO B 535 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO B 535 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 535 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 534 " -0.074 5.00e-02 4.00e+02 1.10e-01 1.92e+01 pdb=" N PRO A 535 " 0.189 5.00e-02 4.00e+02 pdb=" CA PRO A 535 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 535 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 26 " -0.050 5.00e-02 4.00e+02 7.72e-02 9.54e+00 pdb=" N PRO A 27 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 27 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 27 " -0.044 5.00e-02 4.00e+02 ... (remaining 1192 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1122 2.74 - 3.28: 6646 3.28 - 3.82: 11202 3.82 - 4.36: 14235 4.36 - 4.90: 24319 Nonbonded interactions: 57524 Sorted by model distance: nonbonded pdb=" O CYS A 243 " pdb=" OG SER A 247 " model vdw 2.205 3.040 nonbonded pdb=" O CYS B 243 " pdb=" OG SER B 247 " model vdw 2.205 3.040 nonbonded pdb=" O TRP A 284 " pdb=" OG SER A 288 " model vdw 2.228 3.040 nonbonded pdb=" O TRP B 284 " pdb=" OG SER B 288 " model vdw 2.228 3.040 nonbonded pdb=" O PHE B 42 " pdb=" OG1 THR B 46 " model vdw 2.274 3.040 ... (remaining 57519 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 9 through 308 or resid 333 through 364 or resid 381 throug \ h 603)) selection = (chain 'B' and (resid 9 through 161 or resid 233 through 603)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.290 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 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 : 0.011 0.112 7475 Z= 0.478 Angle : 1.230 13.037 10235 Z= 0.617 Chirality : 0.070 0.471 1252 Planarity : 0.011 0.110 1195 Dihedral : 13.789 79.965 2674 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.52 % Favored : 90.25 % Rotamer: Outliers : 0.76 % Allowed : 9.19 % Favored : 90.05 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -7.00 (0.15), residues: 903 helix: -4.58 (0.08), residues: 668 sheet: None (None), residues: 0 loop : -3.89 (0.32), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 107 TYR 0.011 0.002 TYR A 81 PHE 0.028 0.002 PHE A 354 TRP 0.020 0.002 TRP B 572 HIS 0.011 0.003 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.01084 ( 7475) covalent geometry : angle 1.23009 (10235) hydrogen bonds : bond 0.34388 ( 330) hydrogen bonds : angle 10.44901 ( 978) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 137 time to evaluate : 0.252 Fit side-chains REVERT: A 65 MET cc_start: 0.8834 (mtp) cc_final: 0.8578 (mtp) REVERT: A 344 ARG cc_start: 0.7811 (mtp180) cc_final: 0.7576 (mtp85) REVERT: B 65 MET cc_start: 0.8735 (mtp) cc_final: 0.8460 (mtp) REVERT: B 68 MET cc_start: 0.7694 (mtm) cc_final: 0.7453 (mtm) REVERT: B 344 ARG cc_start: 0.7816 (mtp180) cc_final: 0.7570 (mtp85) outliers start: 6 outliers final: 0 residues processed: 139 average time/residue: 0.0848 time to fit residues: 15.8779 Evaluate side-chains 111 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 304 GLN B 160 ASN B 304 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.127551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.104005 restraints weight = 9350.174| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.57 r_work: 0.2987 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7475 Z= 0.158 Angle : 0.759 11.252 10235 Z= 0.381 Chirality : 0.045 0.242 1252 Planarity : 0.008 0.085 1195 Dihedral : 6.853 57.361 1085 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.64 % Allowed : 11.08 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.78 (0.24), residues: 903 helix: -2.29 (0.17), residues: 629 sheet: None (None), residues: 0 loop : -2.59 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 12 TYR 0.013 0.002 TYR A 81 PHE 0.014 0.001 PHE A 287 TRP 0.018 0.001 TRP B 572 HIS 0.008 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7475) covalent geometry : angle 0.75921 (10235) hydrogen bonds : bond 0.05916 ( 330) hydrogen bonds : angle 4.55508 ( 978) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.275 Fit side-chains REVERT: A 157 GLN cc_start: 0.8275 (mt0) cc_final: 0.7881 (mt0) REVERT: B 65 MET cc_start: 0.9249 (mtp) cc_final: 0.8996 (mtp) outliers start: 21 outliers final: 13 residues processed: 131 average time/residue: 0.0696 time to fit residues: 13.1053 Evaluate side-chains 127 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 502 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 52 optimal weight: 0.3980 chunk 68 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 46 optimal weight: 0.0010 chunk 51 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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 = 0.3441 r_free = 0.3441 target = 0.129026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.105317 restraints weight = 9303.844| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.58 r_work: 0.3010 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7475 Z= 0.125 Angle : 0.658 9.950 10235 Z= 0.328 Chirality : 0.043 0.239 1252 Planarity : 0.006 0.074 1195 Dihedral : 5.927 54.148 1085 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.90 % Allowed : 13.22 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.21 (0.28), residues: 903 helix: -0.95 (0.21), residues: 635 sheet: None (None), residues: 0 loop : -2.46 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 12 TYR 0.019 0.002 TYR B 514 PHE 0.014 0.001 PHE B 287 TRP 0.017 0.001 TRP B 572 HIS 0.007 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 7475) covalent geometry : angle 0.65829 (10235) hydrogen bonds : bond 0.04234 ( 330) hydrogen bonds : angle 3.86055 ( 978) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.280 Fit side-chains REVERT: A 34 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6956 (mp0) REVERT: A 155 VAL cc_start: 0.9030 (p) cc_final: 0.8803 (m) REVERT: A 157 GLN cc_start: 0.8387 (mt0) cc_final: 0.8072 (mt0) REVERT: A 243 CYS cc_start: 0.8484 (m) cc_final: 0.8232 (p) REVERT: A 294 ILE cc_start: 0.8994 (mt) cc_final: 0.8732 (mt) REVERT: B 34 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: B 267 GLU cc_start: 0.8671 (tp30) cc_final: 0.8423 (mm-30) REVERT: B 294 ILE cc_start: 0.9039 (mt) cc_final: 0.8793 (mt) outliers start: 23 outliers final: 8 residues processed: 140 average time/residue: 0.0647 time to fit residues: 13.2106 Evaluate side-chains 127 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 384 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3442 r_free = 0.3442 target = 0.128819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.105074 restraints weight = 9286.377| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.56 r_work: 0.2988 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7475 Z= 0.145 Angle : 0.666 9.212 10235 Z= 0.328 Chirality : 0.044 0.234 1252 Planarity : 0.006 0.072 1195 Dihedral : 5.615 45.281 1085 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.15 % Allowed : 14.86 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.29), residues: 903 helix: -0.45 (0.22), residues: 648 sheet: None (None), residues: 0 loop : -2.25 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 12 TYR 0.023 0.002 TYR B 514 PHE 0.016 0.001 PHE A 287 TRP 0.012 0.001 TRP B 572 HIS 0.006 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 7475) covalent geometry : angle 0.66561 (10235) hydrogen bonds : bond 0.04149 ( 330) hydrogen bonds : angle 3.75094 ( 978) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.226 Fit side-chains REVERT: A 294 ILE cc_start: 0.9013 (mt) cc_final: 0.8758 (mt) REVERT: B 34 GLU cc_start: 0.7531 (pm20) cc_final: 0.7069 (mp0) REVERT: B 267 GLU cc_start: 0.8687 (tp30) cc_final: 0.8447 (mm-30) REVERT: B 484 LEU cc_start: 0.9042 (tp) cc_final: 0.8694 (tt) outliers start: 25 outliers final: 21 residues processed: 128 average time/residue: 0.0645 time to fit residues: 12.0490 Evaluate side-chains 130 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 502 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 70 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 0.0170 chunk 58 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.129625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.105667 restraints weight = 9288.485| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.59 r_work: 0.3016 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7475 Z= 0.117 Angle : 0.625 8.688 10235 Z= 0.309 Chirality : 0.042 0.230 1252 Planarity : 0.005 0.067 1195 Dihedral : 5.208 34.534 1085 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.02 % Allowed : 15.87 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.30), residues: 903 helix: -0.06 (0.22), residues: 654 sheet: None (None), residues: 0 loop : -2.16 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 237 TYR 0.026 0.001 TYR B 514 PHE 0.013 0.001 PHE A 287 TRP 0.013 0.001 TRP B 572 HIS 0.007 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 7475) covalent geometry : angle 0.62531 (10235) hydrogen bonds : bond 0.03519 ( 330) hydrogen bonds : angle 3.57122 ( 978) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.279 Fit side-chains REVERT: A 11 ARG cc_start: 0.7356 (mmp80) cc_final: 0.7130 (mmp80) REVERT: A 267 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7817 (tm-30) REVERT: A 294 ILE cc_start: 0.9028 (mt) cc_final: 0.8773 (mt) REVERT: B 34 GLU cc_start: 0.7413 (pm20) cc_final: 0.6979 (mp0) REVERT: B 267 GLU cc_start: 0.8597 (tp30) cc_final: 0.8370 (mm-30) REVERT: B 294 ILE cc_start: 0.9059 (mt) cc_final: 0.8812 (mt) REVERT: B 484 LEU cc_start: 0.9022 (tp) cc_final: 0.8653 (tt) outliers start: 24 outliers final: 16 residues processed: 134 average time/residue: 0.0677 time to fit residues: 13.1715 Evaluate side-chains 131 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 502 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 90 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 82 optimal weight: 0.0970 chunk 4 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN A 460 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.129674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.105509 restraints weight = 9302.562| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.59 r_work: 0.3013 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7475 Z= 0.119 Angle : 0.648 13.820 10235 Z= 0.311 Chirality : 0.043 0.230 1252 Planarity : 0.005 0.066 1195 Dihedral : 5.055 31.247 1085 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.15 % Allowed : 16.12 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.30), residues: 903 helix: 0.14 (0.22), residues: 654 sheet: None (None), residues: 0 loop : -2.08 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 237 TYR 0.025 0.002 TYR B 514 PHE 0.013 0.001 PHE A 287 TRP 0.011 0.001 TRP B 572 HIS 0.007 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 7475) covalent geometry : angle 0.64776 (10235) hydrogen bonds : bond 0.03476 ( 330) hydrogen bonds : angle 3.52617 ( 978) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.251 Fit side-chains REVERT: A 11 ARG cc_start: 0.7400 (mmp80) cc_final: 0.7139 (mmp80) REVERT: A 34 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7005 (mp0) REVERT: A 243 CYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8306 (p) REVERT: A 294 ILE cc_start: 0.9043 (mt) cc_final: 0.8794 (mt) REVERT: A 484 LEU cc_start: 0.9035 (tp) cc_final: 0.8660 (tt) REVERT: B 34 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6906 (mp0) REVERT: B 267 GLU cc_start: 0.8565 (tp30) cc_final: 0.8334 (mm-30) REVERT: B 294 ILE cc_start: 0.9057 (mt) cc_final: 0.8832 (mt) REVERT: B 484 LEU cc_start: 0.9014 (tp) cc_final: 0.8647 (tt) outliers start: 25 outliers final: 21 residues processed: 136 average time/residue: 0.0573 time to fit residues: 11.4115 Evaluate side-chains 142 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 502 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 32 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 61 optimal weight: 0.0470 chunk 79 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 34 optimal weight: 0.2980 chunk 47 optimal weight: 0.9990 chunk 57 optimal weight: 0.0670 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN B 460 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.132654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.108590 restraints weight = 9226.712| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.58 r_work: 0.3044 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7475 Z= 0.111 Angle : 0.628 12.474 10235 Z= 0.302 Chirality : 0.042 0.227 1252 Planarity : 0.005 0.063 1195 Dihedral : 4.911 30.515 1085 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.90 % Allowed : 15.74 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.30), residues: 903 helix: 0.31 (0.22), residues: 655 sheet: None (None), residues: 0 loop : -2.06 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 237 TYR 0.024 0.001 TYR B 514 PHE 0.012 0.001 PHE A 287 TRP 0.012 0.001 TRP B 572 HIS 0.006 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 7475) covalent geometry : angle 0.62794 (10235) hydrogen bonds : bond 0.03171 ( 330) hydrogen bonds : angle 3.44088 ( 978) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.280 Fit side-chains REVERT: A 34 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6964 (mp0) REVERT: A 243 CYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8360 (p) REVERT: A 270 ASN cc_start: 0.8183 (m-40) cc_final: 0.7916 (m-40) REVERT: A 294 ILE cc_start: 0.9056 (mt) cc_final: 0.8816 (mt) REVERT: A 484 LEU cc_start: 0.9027 (tp) cc_final: 0.8643 (tt) REVERT: B 34 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6866 (mp0) REVERT: B 294 ILE cc_start: 0.9053 (mt) cc_final: 0.8851 (mt) REVERT: B 484 LEU cc_start: 0.9056 (tp) cc_final: 0.8690 (tt) outliers start: 23 outliers final: 18 residues processed: 135 average time/residue: 0.0623 time to fit residues: 12.0749 Evaluate side-chains 142 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 502 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 37 optimal weight: 0.7980 chunk 72 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 chunk 30 optimal weight: 0.0040 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 80 optimal weight: 0.2980 chunk 68 optimal weight: 1.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN A 460 ASN B 460 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.131617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.107344 restraints weight = 9230.246| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.58 r_work: 0.3021 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7475 Z= 0.118 Angle : 0.640 11.879 10235 Z= 0.306 Chirality : 0.043 0.225 1252 Planarity : 0.005 0.065 1195 Dihedral : 4.903 30.426 1085 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.15 % Allowed : 15.49 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.30), residues: 903 helix: 0.38 (0.22), residues: 659 sheet: None (None), residues: 0 loop : -2.01 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 12 TYR 0.022 0.001 TYR A 514 PHE 0.013 0.001 PHE A 287 TRP 0.011 0.001 TRP B 572 HIS 0.007 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 7475) covalent geometry : angle 0.63986 (10235) hydrogen bonds : bond 0.03329 ( 330) hydrogen bonds : angle 3.44426 ( 978) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.258 Fit side-chains REVERT: A 34 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7047 (mp0) REVERT: A 243 CYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8413 (p) REVERT: A 270 ASN cc_start: 0.8185 (m-40) cc_final: 0.7926 (m-40) REVERT: A 294 ILE cc_start: 0.9062 (mt) cc_final: 0.8830 (mt) REVERT: A 484 LEU cc_start: 0.9074 (tp) cc_final: 0.8691 (tt) REVERT: B 34 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6856 (mp0) REVERT: B 484 LEU cc_start: 0.9068 (tp) cc_final: 0.8700 (tt) outliers start: 25 outliers final: 20 residues processed: 136 average time/residue: 0.0598 time to fit residues: 11.8744 Evaluate side-chains 139 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 502 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 86 optimal weight: 0.3980 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 34 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN B 304 GLN B 460 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.130567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.106055 restraints weight = 9125.409| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.59 r_work: 0.3016 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7475 Z= 0.122 Angle : 0.645 11.450 10235 Z= 0.309 Chirality : 0.043 0.224 1252 Planarity : 0.005 0.065 1195 Dihedral : 4.918 30.116 1085 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.90 % Allowed : 16.88 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.30), residues: 903 helix: 0.42 (0.22), residues: 660 sheet: None (None), residues: 0 loop : -2.06 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 12 TYR 0.010 0.001 TYR A 514 PHE 0.013 0.001 PHE B 287 TRP 0.010 0.001 TRP B 572 HIS 0.007 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7475) covalent geometry : angle 0.64488 (10235) hydrogen bonds : bond 0.03390 ( 330) hydrogen bonds : angle 3.45158 ( 978) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.256 Fit side-chains REVERT: A 34 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: A 294 ILE cc_start: 0.9065 (mt) cc_final: 0.8854 (mt) REVERT: A 484 LEU cc_start: 0.9080 (tp) cc_final: 0.8698 (tt) REVERT: B 34 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6919 (mp0) REVERT: B 484 LEU cc_start: 0.9083 (tp) cc_final: 0.8699 (tt) outliers start: 23 outliers final: 20 residues processed: 134 average time/residue: 0.0591 time to fit residues: 11.6390 Evaluate side-chains 136 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 502 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 6 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 74 optimal weight: 0.0870 chunk 27 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 57 optimal weight: 0.0170 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN B 460 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.132557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.108243 restraints weight = 9070.160| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.58 r_work: 0.3037 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7475 Z= 0.112 Angle : 0.635 11.083 10235 Z= 0.303 Chirality : 0.042 0.224 1252 Planarity : 0.005 0.064 1195 Dihedral : 4.829 30.050 1085 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.64 % Allowed : 16.88 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.30), residues: 903 helix: 0.51 (0.22), residues: 660 sheet: None (None), residues: 0 loop : -2.05 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 12 TYR 0.008 0.001 TYR B 81 PHE 0.012 0.001 PHE B 287 TRP 0.012 0.001 TRP B 572 HIS 0.007 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 7475) covalent geometry : angle 0.63523 (10235) hydrogen bonds : bond 0.03148 ( 330) hydrogen bonds : angle 3.39033 ( 978) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.283 Fit side-chains REVERT: A 34 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6900 (mp0) REVERT: A 484 LEU cc_start: 0.9064 (tp) cc_final: 0.8677 (tt) REVERT: B 34 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6890 (mp0) REVERT: B 484 LEU cc_start: 0.9083 (tp) cc_final: 0.8725 (tt) outliers start: 21 outliers final: 19 residues processed: 138 average time/residue: 0.0648 time to fit residues: 13.1173 Evaluate side-chains 142 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 502 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 83 optimal weight: 0.0980 chunk 39 optimal weight: 0.9980 chunk 3 optimal weight: 0.1980 chunk 18 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 61 optimal weight: 0.0010 chunk 70 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 0.0370 overall best weight: 0.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN B 460 ASN B 558 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.137688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.113873 restraints weight = 9094.106| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.55 r_work: 0.3078 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 7475 Z= 0.108 Angle : 0.625 10.723 10235 Z= 0.298 Chirality : 0.041 0.222 1252 Planarity : 0.005 0.063 1195 Dihedral : 4.696 29.166 1085 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.27 % Allowed : 17.88 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.30), residues: 903 helix: 0.60 (0.22), residues: 660 sheet: None (None), residues: 0 loop : -2.08 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 11 TYR 0.009 0.001 TYR B 39 PHE 0.011 0.001 PHE A 287 TRP 0.023 0.001 TRP B 305 HIS 0.006 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 7475) covalent geometry : angle 0.62488 (10235) hydrogen bonds : bond 0.02881 ( 330) hydrogen bonds : angle 3.33828 ( 978) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1674.31 seconds wall clock time: 29 minutes 21.13 seconds (1761.13 seconds total)