Starting phenix.real_space_refine on Thu Jul 2 06:32:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w6h_37323/07_2026/8w6h_37323.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w6h_37323/07_2026/8w6h_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 { model { file = "/net/cci-nas-00/data/ceres_data/8w6h_37323/07_2026/8w6h_37323.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w6h_37323/07_2026/8w6h_37323.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w6h_37323/07_2026/8w6h_37323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w6h_37323/07_2026/8w6h_37323.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 33 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'CLR': 1, 'SO4': 1} Classifications: {'undetermined': 2} Chain breaks: 1 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'CLR': 1, 'SO4': 1} Classifications: {'undetermined': 2} Chain breaks: 1 Time building chain proxies: 1.83, per 1000 atoms: 0.25 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: 0.52 Conformation dependent library (CDL) restraints added in 368.8 milliseconds 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: 0.16 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: 0.81 Time building geometry restraints manager: 0.74 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: 1.250 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.770 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 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 are 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/Z covalent geometry : bond 0.01084 / 0.48 ( 7475) covalent geometry : angle 1.23009 / 0.62 (10235) hydrogen bonds : bond 0.34388 / 22.08 ( 330) hydrogen bonds : angle 10.44901 / 7.21 ( 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 : 0.179 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: 0.0885 time to fit residues: 16.6250 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 : 0.284 ------------------------------------------------------------------------------- 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... 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 = 0.3416 r_free = 0.3416 target = 0.126893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.103398 restraints weight = 9349.399| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.57 r_work: 0.2988 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7475 Z= 0.158 Angle : 0.761 11.361 10235 Z= 0.382 Chirality : 0.045 0.252 1252 Planarity : 0.008 0.085 1195 Dihedral : 6.904 56.471 1085 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.27 % Allowed : 10.96 % Favored : 86.78 % 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 are not related in a simple way. whole: -3.79 (0.24), residues: 903 helix: -2.29 (0.17), residues: 635 sheet: None (None), residues: 0 loop : -2.59 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 12 TYR 0.012 0.002 TYR A 81 PHE 0.014 0.001 PHE B 287 TRP 0.018 0.001 TRP B 572 HIS 0.008 0.001 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 7475) covalent geometry : angle 0.76062 / 0.38 (10235) hydrogen bonds : bond 0.06219 / 4.04 ( 330) hydrogen bonds : angle 4.57666 / 3.10 ( 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: 18 poor density : 123 time to evaluate : 0.291 Fit side-chains REVERT: A 157 GLN cc_start: 0.8285 (mt0) cc_final: 0.7906 (mt0) REVERT: B 65 MET cc_start: 0.9266 (mtp) cc_final: 0.9012 (mtp) outliers start: 18 outliers final: 11 residues processed: 132 average time/residue: 0.0738 time to fit residues: 14.0369 Evaluate side-chains 125 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 52 optimal weight: 8.9990 chunk 68 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 33 optimal weight: 0.0070 chunk 54 optimal weight: 2.9990 chunk 45 optimal weight: 0.0980 chunk 46 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.129338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.105782 restraints weight = 9261.037| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.57 r_work: 0.3017 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7475 Z= 0.120 Angle : 0.659 10.031 10235 Z= 0.328 Chirality : 0.043 0.237 1252 Planarity : 0.006 0.075 1195 Dihedral : 6.079 56.180 1085 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.02 % Allowed : 13.10 % 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 are not related in a simple way. whole: -2.25 (0.28), residues: 903 helix: -0.95 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -2.54 (0.36), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 11 TYR 0.022 0.002 TYR A 514 PHE 0.013 0.001 PHE B 287 TRP 0.016 0.001 TRP A 572 HIS 0.006 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 7475) covalent geometry : angle 0.65880 / 0.33 (10235) hydrogen bonds : bond 0.04248 / 2.80 ( 330) hydrogen bonds : angle 3.90319 / 2.64 ( 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: 24 poor density : 126 time to evaluate : 0.300 Fit side-chains REVERT: A 11 ARG cc_start: 0.7439 (mmp80) cc_final: 0.7176 (mmp80) REVERT: A 155 VAL cc_start: 0.9023 (p) cc_final: 0.8782 (m) REVERT: A 157 GLN cc_start: 0.8407 (mt0) cc_final: 0.8090 (mt0) REVERT: A 267 GLU cc_start: 0.8661 (tp30) cc_final: 0.8419 (mm-30) REVERT: A 294 ILE cc_start: 0.8998 (mt) cc_final: 0.8749 (mt) REVERT: B 34 GLU cc_start: 0.7470 (pm20) cc_final: 0.7045 (mp0) REVERT: B 267 GLU cc_start: 0.8644 (tp30) cc_final: 0.8424 (mm-30) REVERT: B 294 ILE cc_start: 0.9041 (mt) cc_final: 0.8785 (mt) outliers start: 24 outliers final: 11 residues processed: 141 average time/residue: 0.0692 time to fit residues: 14.3164 Evaluate side-chains 123 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 84 ASP Chi-restraints excluded: chain A residue 306 LEU 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 115 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 502 SER 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: 1.9990 chunk 41 optimal weight: 0.0770 chunk 86 optimal weight: 0.3980 chunk 50 optimal weight: 0.0980 chunk 80 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.129693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.105913 restraints weight = 9267.445| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.57 r_work: 0.3006 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2386 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= 0.127 Angle : 0.647 9.145 10235 Z= 0.320 Chirality : 0.043 0.230 1252 Planarity : 0.005 0.072 1195 Dihedral : 5.559 45.929 1085 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.27 % Allowed : 14.99 % Favored : 81.74 % 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 are not related in a simple way. whole: -1.55 (0.29), residues: 903 helix: -0.42 (0.22), residues: 646 sheet: None (None), residues: 0 loop : -2.37 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 12 TYR 0.010 0.001 TYR A 81 PHE 0.015 0.001 PHE B 287 TRP 0.013 0.001 TRP B 572 HIS 0.006 0.001 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 7475) covalent geometry : angle 0.64743 / 0.32 (10235) hydrogen bonds : bond 0.03923 / 2.59 ( 330) hydrogen bonds : angle 3.70274 / 2.50 ( 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 140 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.277 Fit side-chains REVERT: A 11 ARG cc_start: 0.7460 (mmp80) cc_final: 0.7216 (mmp80) REVERT: A 34 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: A 157 GLN cc_start: 0.8251 (mt0) cc_final: 0.7991 (mt0) REVERT: A 294 ILE cc_start: 0.9022 (mt) cc_final: 0.8764 (mt) REVERT: B 34 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7046 (mp0) REVERT: B 243 CYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8277 (p) REVERT: B 267 GLU cc_start: 0.8642 (tp30) cc_final: 0.8426 (mm-30) REVERT: B 294 ILE cc_start: 0.9076 (mt) cc_final: 0.8839 (mt) outliers start: 26 outliers final: 18 residues processed: 130 average time/residue: 0.0704 time to fit residues: 13.4004 Evaluate side-chains 131 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 34 GLU 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 270 ASN Chi-restraints excluded: chain A residue 306 LEU 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 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 235 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 253 LEU 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: 0.6980 chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 47 optimal weight: 0.3980 chunk 39 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 460 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.129088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.105128 restraints weight = 9336.609| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.60 r_work: 0.3013 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7475 Z= 0.124 Angle : 0.634 8.786 10235 Z= 0.313 Chirality : 0.043 0.231 1252 Planarity : 0.005 0.069 1195 Dihedral : 5.254 36.529 1085 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.65 % Allowed : 15.49 % Favored : 80.86 % 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 are not related in a simple way. whole: -1.09 (0.30), residues: 903 helix: -0.06 (0.22), residues: 643 sheet: None (None), residues: 0 loop : -2.25 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 12 TYR 0.010 0.001 TYR A 81 PHE 0.014 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/Z covalent geometry : bond 0.00297 / 0.12 ( 7475) covalent geometry : angle 0.63384 / 0.31 (10235) hydrogen bonds : bond 0.03673 / 2.42 ( 330) hydrogen bonds : angle 3.62837 / 2.45 ( 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 144 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.282 Fit side-chains REVERT: A 34 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7016 (mp0) REVERT: A 267 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7766 (tm-30) REVERT: A 294 ILE cc_start: 0.9039 (mt) cc_final: 0.8795 (mt) REVERT: B 34 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7016 (mp0) REVERT: B 243 CYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8426 (p) REVERT: B 267 GLU cc_start: 0.8604 (tp30) cc_final: 0.8386 (mm-30) REVERT: B 294 ILE cc_start: 0.9058 (mt) cc_final: 0.8814 (mt) REVERT: B 484 LEU cc_start: 0.9027 (tp) cc_final: 0.8667 (tt) outliers start: 29 outliers final: 17 residues processed: 133 average time/residue: 0.0680 time to fit residues: 13.1939 Evaluate side-chains 134 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 34 GLU 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 306 LEU 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 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 235 VAL Chi-restraints excluded: chain B residue 243 CYS 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: 0.8980 chunk 49 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 82 optimal weight: 0.0870 chunk 4 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 460 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.130825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.107312 restraints weight = 9260.325| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.56 r_work: 0.3022 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7475 Z= 0.122 Angle : 0.653 14.687 10235 Z= 0.313 Chirality : 0.043 0.226 1252 Planarity : 0.005 0.066 1195 Dihedral : 5.071 31.574 1085 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.27 % Allowed : 16.62 % Favored : 80.10 % 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 are not related in a simple way. whole: -0.92 (0.30), residues: 903 helix: 0.08 (0.22), residues: 656 sheet: None (None), residues: 0 loop : -2.34 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 11 TYR 0.025 0.001 TYR A 514 PHE 0.013 0.001 PHE A 287 TRP 0.012 0.001 TRP B 572 HIS 0.007 0.001 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 ( 7475) covalent geometry : angle 0.65300 / 0.31 (10235) hydrogen bonds : bond 0.03531 / 2.34 ( 330) hydrogen bonds : angle 3.54777 / 2.39 ( 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 143 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.278 Fit side-chains REVERT: A 34 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: A 294 ILE cc_start: 0.9052 (mt) cc_final: 0.8806 (mt) REVERT: A 484 LEU cc_start: 0.9027 (tp) cc_final: 0.8655 (tt) REVERT: B 34 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6914 (mp0) REVERT: B 243 CYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8432 (p) REVERT: B 267 GLU cc_start: 0.8559 (tp30) cc_final: 0.8330 (mm-30) REVERT: B 294 ILE cc_start: 0.9069 (mt) cc_final: 0.8845 (mt) REVERT: B 484 LEU cc_start: 0.9048 (tp) cc_final: 0.8683 (tt) outliers start: 26 outliers final: 19 residues processed: 134 average time/residue: 0.0669 time to fit residues: 13.1383 Evaluate side-chains 137 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 306 LEU 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 235 VAL Chi-restraints excluded: chain B residue 243 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 32 optimal weight: 0.7980 chunk 66 optimal weight: 0.0020 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 74 optimal weight: 0.0980 chunk 42 optimal weight: 0.0870 chunk 69 optimal weight: 0.1980 chunk 82 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 47 optimal weight: 0.2980 chunk 57 optimal weight: 0.5980 overall best weight: 0.1366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 460 ASN B 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.133751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.109575 restraints weight = 9262.840| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.62 r_work: 0.3077 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7475 Z= 0.107 Angle : 0.624 12.283 10235 Z= 0.300 Chirality : 0.041 0.222 1252 Planarity : 0.005 0.063 1195 Dihedral : 4.842 30.692 1085 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.77 % Allowed : 16.88 % Favored : 80.35 % 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 are not related in a simple way. whole: -0.63 (0.30), residues: 903 helix: 0.33 (0.22), residues: 652 sheet: None (None), residues: 0 loop : -2.32 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 11 TYR 0.008 0.001 TYR A 39 PHE 0.011 0.001 PHE A 287 TRP 0.013 0.001 TRP B 572 HIS 0.006 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 7475) covalent geometry : angle 0.62398 / 0.30 (10235) hydrogen bonds : bond 0.02980 / 1.98 ( 330) hydrogen bonds : angle 3.41579 / 2.31 ( 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 151 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.284 Fit side-chains REVERT: A 34 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6916 (mp0) REVERT: A 243 CYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8326 (p) REVERT: A 267 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7847 (tm-30) REVERT: A 270 ASN cc_start: 0.8146 (m-40) cc_final: 0.7877 (t0) REVERT: A 294 ILE cc_start: 0.9031 (mt) cc_final: 0.8820 (mt) REVERT: A 484 LEU cc_start: 0.8995 (tp) cc_final: 0.8606 (tt) REVERT: B 34 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: B 243 CYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8465 (p) REVERT: B 267 GLU cc_start: 0.8608 (tp30) cc_final: 0.8387 (mm-30) REVERT: B 484 LEU cc_start: 0.9014 (tp) cc_final: 0.8631 (tt) outliers start: 22 outliers final: 11 residues processed: 142 average time/residue: 0.0675 time to fit residues: 14.0923 Evaluate side-chains 135 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 155 VAL Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 267 GLU 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 115 MET Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 308 LEU 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: 0.6980 chunk 72 optimal weight: 8.9990 chunk 65 optimal weight: 0.4980 chunk 30 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3466 r_free = 0.3466 target = 0.130822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.106607 restraints weight = 9298.269| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.59 r_work: 0.3028 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2818 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= 0.127 Angle : 0.650 11.939 10235 Z= 0.311 Chirality : 0.043 0.221 1252 Planarity : 0.005 0.064 1195 Dihedral : 4.910 30.503 1085 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.14 % Allowed : 17.51 % Favored : 80.35 % 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 are not related in a simple way. whole: -0.57 (0.30), residues: 903 helix: 0.33 (0.22), residues: 659 sheet: None (None), residues: 0 loop : -2.22 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 12 TYR 0.020 0.001 TYR B 514 PHE 0.014 0.001 PHE B 287 TRP 0.019 0.001 TRP B 305 HIS 0.007 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 7475) covalent geometry : angle 0.65044 / 0.31 (10235) hydrogen bonds : bond 0.03516 / 2.31 ( 330) hydrogen bonds : angle 3.48636 / 2.35 ( 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 141 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.239 Fit side-chains REVERT: A 34 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7035 (mp0) REVERT: A 243 CYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8389 (p) REVERT: A 294 ILE cc_start: 0.9050 (mt) cc_final: 0.8829 (mt) REVERT: A 484 LEU cc_start: 0.9089 (tp) cc_final: 0.8684 (tt) REVERT: B 34 GLU cc_start: 0.7371 (pm20) cc_final: 0.6902 (mp0) REVERT: B 243 CYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8497 (p) REVERT: B 267 GLU cc_start: 0.8621 (tp30) cc_final: 0.8397 (mm-30) REVERT: B 305 TRP cc_start: 0.8718 (t60) cc_final: 0.8159 (t60) REVERT: B 484 LEU cc_start: 0.9072 (tp) cc_final: 0.8698 (tt) outliers start: 17 outliers final: 13 residues processed: 134 average time/residue: 0.0608 time to fit residues: 11.7992 Evaluate side-chains 132 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.170 ------------------------------------------------------------------------------- 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 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 55 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 308 LEU 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: 1.9990 chunk 16 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 86 optimal weight: 0.0050 chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3426 r_free = 0.3426 target = 0.127777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.103563 restraints weight = 9225.263| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.58 r_work: 0.2978 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7475 Z= 0.161 Angle : 0.684 11.625 10235 Z= 0.329 Chirality : 0.045 0.221 1252 Planarity : 0.005 0.067 1195 Dihedral : 5.138 30.279 1085 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.02 % Allowed : 18.26 % Favored : 79.72 % 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 are not related in a simple way. whole: -0.72 (0.30), residues: 903 helix: 0.23 (0.22), residues: 655 sheet: None (None), residues: 0 loop : -2.26 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 12 TYR 0.011 0.001 TYR A 345 PHE 0.018 0.001 PHE B 354 TRP 0.018 0.001 TRP B 305 HIS 0.009 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.16 ( 7475) covalent geometry : angle 0.68435 / 0.33 (10235) hydrogen bonds : bond 0.03989 / 2.60 ( 330) hydrogen bonds : angle 3.66605 / 2.47 ( 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 130 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.350 Fit side-chains REVERT: A 243 CYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8459 (p) REVERT: A 484 LEU cc_start: 0.9121 (tp) cc_final: 0.8723 (tt) REVERT: B 305 TRP cc_start: 0.8850 (t60) cc_final: 0.8261 (t60) REVERT: B 484 LEU cc_start: 0.9113 (tp) cc_final: 0.8745 (tt) outliers start: 16 outliers final: 14 residues processed: 125 average time/residue: 0.0661 time to fit residues: 11.9786 Evaluate side-chains 127 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 55 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 243 CYS 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 55 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: 7.9990 chunk 8 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 0.0870 chunk 39 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3472 r_free = 0.3472 target = 0.130961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.106965 restraints weight = 9080.249| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.57 r_work: 0.3014 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2854 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= 0.125 Angle : 0.655 11.288 10235 Z= 0.315 Chirality : 0.043 0.223 1252 Planarity : 0.005 0.065 1195 Dihedral : 5.045 30.305 1085 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.64 % Allowed : 19.27 % Favored : 79.09 % 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 are not related in a simple way. whole: -0.54 (0.30), residues: 903 helix: 0.36 (0.22), residues: 654 sheet: None (None), residues: 0 loop : -2.19 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 12 TYR 0.025 0.001 TYR A 514 PHE 0.014 0.001 PHE B 287 TRP 0.017 0.001 TRP B 305 HIS 0.008 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 7475) covalent geometry : angle 0.65541 / 0.31 (10235) hydrogen bonds : bond 0.03546 / 2.33 ( 330) hydrogen bonds : angle 3.56772 / 2.41 ( 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 132 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.263 Fit side-chains REVERT: A 484 LEU cc_start: 0.9087 (tp) cc_final: 0.8698 (tt) REVERT: B 305 TRP cc_start: 0.8801 (t60) cc_final: 0.8180 (t60) REVERT: B 484 LEU cc_start: 0.9101 (tp) cc_final: 0.8738 (tt) outliers start: 13 outliers final: 11 residues processed: 128 average time/residue: 0.0592 time to fit residues: 11.0374 Evaluate side-chains 128 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 55 LEU Chi-restraints excluded: chain A residue 155 VAL 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 55 LEU 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: 0.5980 chunk 39 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 chunk 18 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 30 optimal weight: 0.2980 chunk 61 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3470 r_free = 0.3470 target = 0.131030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.106746 restraints weight = 9218.458| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.60 r_work: 0.3032 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2985 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= 0.117 Angle : 0.644 10.929 10235 Z= 0.310 Chirality : 0.042 0.224 1252 Planarity : 0.005 0.065 1195 Dihedral : 4.906 29.815 1085 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.89 % Allowed : 19.14 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.30), residues: 903 helix: 0.46 (0.22), residues: 653 sheet: None (None), residues: 0 loop : -2.20 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 12 TYR 0.009 0.001 TYR A 81 PHE 0.013 0.001 PHE A 287 TRP 0.016 0.001 TRP B 305 HIS 0.007 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 7475) covalent geometry : angle 0.64424 / 0.31 (10235) hydrogen bonds : bond 0.03279 / 2.16 ( 330) hydrogen bonds : angle 3.49795 / 2.37 ( 978) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1800.84 seconds wall clock time: 31 minutes 41.57 seconds (1901.57 seconds total)