Starting phenix.real_space_refine on Sat Jul 4 10:43:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zpl_14857/07_2026/7zpl_14857.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zpl_14857/07_2026/7zpl_14857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zpl_14857/07_2026/7zpl_14857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zpl_14857/07_2026/7zpl_14857.map" model { file = "/net/cci-nas-00/data/ceres_data/7zpl_14857/07_2026/7zpl_14857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zpl_14857/07_2026/7zpl_14857.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7zpl_14857/07_2026/7zpl_14857.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zpl_14857/07_2026/7zpl_14857.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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: 6 Type Number sf(0) Gaussians P 24 5.49 5 Mg 1 5.21 5 S 148 5.16 5 C 12498 2.51 5 N 3440 2.21 5 O 3808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s 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: 19919 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4133 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 28, 'TRANS': 485} Chain: "B" Number of atoms: 4914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 618, 4914 Classifications: {'peptide': 618} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 589} Chain breaks: 2 Chain: "C" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 650 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 6, 'TRANS': 72} Chain: "V" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 262 Classifications: {'RNA': 12} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 8} Chain: "D" Number of atoms: 4133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4133 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 28, 'TRANS': 485} Chain: "E" Number of atoms: 4914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 618, 4914 Classifications: {'peptide': 618} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 589} Chain breaks: 2 Chain: "F" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 650 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 6, 'TRANS': 72} Chain: "U" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 262 Classifications: {'RNA': 12} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 8} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.33, per 1000 atoms: 0.22 Number of scatterers: 19919 At special positions: 0 Unit cell: (177.24, 131.04, 97.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 148 16.00 P 24 15.00 Mg 1 11.99 O 3808 8.00 N 3440 7.00 C 12498 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 629.8 milliseconds 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4564 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 23 sheets defined 49.1% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 302 through 313 removed outlier: 3.934A pdb=" N ASP A 306 " --> pdb=" O ILE A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 350 removed outlier: 3.816A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 381 through 385 removed outlier: 3.792A pdb=" N LYS A 385 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.587A pdb=" N SER A 409 " --> pdb=" O CYS A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 451 removed outlier: 3.834A pdb=" N GLU A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 476 removed outlier: 3.715A pdb=" N GLU A 457 " --> pdb=" O CYS A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.841A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 582 through 602 removed outlier: 3.535A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N MET A 595 " --> pdb=" O GLN A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 613 removed outlier: 3.567A pdb=" N PHE A 612 " --> pdb=" O THR A 608 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A 613 " --> pdb=" O LYS A 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 608 through 613' Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 4.130A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 693 removed outlier: 3.526A pdb=" N LEU A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N CYS A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 714 Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.619A pdb=" N THR B 20 " --> pdb=" O ALA B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 116 Processing helix chain 'B' and resid 119 through 123 removed outlier: 3.642A pdb=" N LEU B 122 " --> pdb=" O VAL B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.511A pdb=" N MET B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 248 through 265 removed outlier: 3.890A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 291 Processing helix chain 'B' and resid 309 through 313 removed outlier: 4.053A pdb=" N GLN B 313 " --> pdb=" O ASN B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 removed outlier: 3.541A pdb=" N PHE B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 345 removed outlier: 4.331A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 371 through 375 removed outlier: 3.859A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 413 through 426 removed outlier: 3.579A pdb=" N ILE B 423 " --> pdb=" O LEU B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 455 through 474 removed outlier: 3.520A pdb=" N VAL B 473 " --> pdb=" O THR B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 537 Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 600 through 604 Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 613 through 616 Processing helix chain 'B' and resid 617 through 625 removed outlier: 3.551A pdb=" N CYS B 625 " --> pdb=" O GLN B 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 52 Processing helix chain 'C' and resid 62 through 67 removed outlier: 3.622A pdb=" N MET C 66 " --> pdb=" O ARG C 62 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 67' Processing helix chain 'C' and resid 92 through 102 removed outlier: 3.786A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'D' and resid 208 through 217 Processing helix chain 'D' and resid 225 through 235 Processing helix chain 'D' and resid 240 through 249 Processing helix chain 'D' and resid 302 through 313 removed outlier: 3.934A pdb=" N ASP D 306 " --> pdb=" O ILE D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 350 removed outlier: 3.816A pdb=" N TYR D 334 " --> pdb=" O ILE D 330 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE D 348 " --> pdb=" O GLU D 344 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN D 350 " --> pdb=" O GLN D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 370 Processing helix chain 'D' and resid 381 through 385 removed outlier: 3.790A pdb=" N LYS D 385 " --> pdb=" O GLU D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 415 removed outlier: 3.586A pdb=" N SER D 409 " --> pdb=" O CYS D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 451 removed outlier: 3.835A pdb=" N GLU D 449 " --> pdb=" O TYR D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 476 removed outlier: 3.715A pdb=" N GLU D 457 " --> pdb=" O CYS D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 538 removed outlier: 3.842A pdb=" N GLU D 538 " --> pdb=" O HIS D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 579 Processing helix chain 'D' and resid 582 through 602 removed outlier: 3.534A pdb=" N LEU D 586 " --> pdb=" O ARG D 582 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER D 594 " --> pdb=" O GLN D 590 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N MET D 595 " --> pdb=" O GLN D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 613 removed outlier: 3.566A pdb=" N PHE D 612 " --> pdb=" O THR D 608 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU D 613 " --> pdb=" O LYS D 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 608 through 613' Processing helix chain 'D' and resid 632 through 650 Processing helix chain 'D' and resid 652 through 674 removed outlier: 4.130A pdb=" N LYS D 664 " --> pdb=" O ALA D 660 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU D 665 " --> pdb=" O GLU D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 693 removed outlier: 3.526A pdb=" N LEU D 686 " --> pdb=" O ASP D 682 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N CYS D 693 " --> pdb=" O ALA D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 714 Processing helix chain 'E' and resid 5 through 11 Processing helix chain 'E' and resid 17 through 22 removed outlier: 3.618A pdb=" N THR E 20 " --> pdb=" O ALA E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 49 Processing helix chain 'E' and resid 84 through 99 Processing helix chain 'E' and resid 101 through 116 Processing helix chain 'E' and resid 119 through 123 removed outlier: 3.641A pdb=" N LEU E 122 " --> pdb=" O VAL E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 153 Processing helix chain 'E' and resid 162 through 174 removed outlier: 3.511A pdb=" N MET E 174 " --> pdb=" O VAL E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 222 Processing helix chain 'E' and resid 248 through 265 removed outlier: 3.891A pdb=" N LYS E 265 " --> pdb=" O SER E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 291 Processing helix chain 'E' and resid 309 through 313 removed outlier: 4.053A pdb=" N GLN E 313 " --> pdb=" O ASN E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 326 removed outlier: 3.541A pdb=" N PHE E 318 " --> pdb=" O ASN E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 345 removed outlier: 4.332A pdb=" N ALA E 340 " --> pdb=" O VAL E 336 " (cutoff:3.500A) Proline residue: E 341 - end of helix Processing helix chain 'E' and resid 371 through 375 removed outlier: 3.859A pdb=" N ALA E 374 " --> pdb=" O GLU E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 393 Processing helix chain 'E' and resid 413 through 426 removed outlier: 3.579A pdb=" N ILE E 423 " --> pdb=" O LEU E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 433 Processing helix chain 'E' and resid 455 through 474 removed outlier: 3.520A pdb=" N VAL E 473 " --> pdb=" O THR E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 537 Processing helix chain 'E' and resid 540 through 560 Processing helix chain 'E' and resid 572 through 583 Processing helix chain 'E' and resid 585 through 589 Processing helix chain 'E' and resid 590 through 594 Processing helix chain 'E' and resid 600 through 604 Processing helix chain 'E' and resid 607 through 612 Processing helix chain 'E' and resid 613 through 616 Processing helix chain 'E' and resid 617 through 625 removed outlier: 3.552A pdb=" N CYS E 625 " --> pdb=" O GLN E 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 52 Processing helix chain 'F' and resid 62 through 67 removed outlier: 3.622A pdb=" N MET F 66 " --> pdb=" O ARG F 62 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE F 67 " --> pdb=" O ILE F 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 67' Processing helix chain 'F' and resid 92 through 102 removed outlier: 3.787A pdb=" N VAL F 96 " --> pdb=" O SER F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 115 Processing sheet with id=AA1, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA2, first strand: chain 'A' and resid 290 through 292 removed outlier: 7.397A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 526 " --> pdb=" O PHE A 562 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLY A 555 " --> pdb=" O ARG A 551 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG A 551 " --> pdb=" O GLY A 555 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL A 557 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LEU A 549 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL A 542 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN A 321 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY A 546 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLU A 319 " --> pdb=" O GLY A 546 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N MET A 548 " --> pdb=" O TRP A 317 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N TRP A 317 " --> pdb=" O MET A 548 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 292 removed outlier: 5.354A pdb=" N THR A 498 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N CYS A 489 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN A 481 " --> pdb=" O LYS A 506 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 353 through 355 Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 378 removed outlier: 5.913A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N GLN B 367 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 628 through 631 removed outlier: 6.508A pdb=" N GLU A 629 " --> pdb=" O ILE A 621 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AA9, first strand: chain 'B' and resid 178 through 179 Processing sheet with id=AB1, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.845A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 489 through 492 removed outlier: 3.594A pdb=" N PHE B 496 " --> pdb=" O ALA B 503 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 667 through 668 removed outlier: 4.912A pdb=" N ILE B 667 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N MET C 90 " --> pdb=" O SER C 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 258 through 259 Processing sheet with id=AB5, first strand: chain 'D' and resid 290 through 292 removed outlier: 7.397A pdb=" N TYR D 501 " --> pdb=" O PHE D 525 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER D 526 " --> pdb=" O PHE D 562 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLY D 555 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG D 551 " --> pdb=" O GLY D 555 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL D 557 " --> pdb=" O LEU D 549 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LEU D 549 " --> pdb=" O VAL D 557 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ARG D 559 " --> pdb=" O ASP D 547 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASP D 547 " --> pdb=" O ARG D 559 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N MET D 561 " --> pdb=" O ILE D 545 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL D 542 " --> pdb=" O ILE D 323 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN D 321 " --> pdb=" O GLU D 544 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY D 546 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N GLU D 319 " --> pdb=" O GLY D 546 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N MET D 548 " --> pdb=" O TRP D 317 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N TRP D 317 " --> pdb=" O MET D 548 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 290 through 292 removed outlier: 5.354A pdb=" N THR D 498 " --> pdb=" O CYS D 489 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N CYS D 489 " --> pdb=" O THR D 498 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N LEU D 500 " --> pdb=" O SER D 487 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER D 487 " --> pdb=" O LEU D 500 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY D 502 " --> pdb=" O MET D 485 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN D 481 " --> pdb=" O LYS D 506 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE D 480 " --> pdb=" O MET D 360 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 377 through 378 removed outlier: 6.014A pdb=" N GLU D 377 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N GLN E 367 " --> pdb=" O GLU D 377 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 628 through 631 removed outlier: 6.508A pdb=" N GLU D 629 " --> pdb=" O ILE D 621 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 54 through 57 Processing sheet with id=AC1, first strand: chain 'E' and resid 128 through 130 Processing sheet with id=AC2, first strand: chain 'E' and resid 178 through 179 Processing sheet with id=AC3, first strand: chain 'E' and resid 240 through 243 removed outlier: 6.845A pdb=" N LEU E 224 " --> pdb=" O ARG E 350 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 489 through 492 removed outlier: 3.594A pdb=" N PHE E 496 " --> pdb=" O ALA E 503 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 57 through 59 removed outlier: 4.134A pdb=" N MET F 90 " --> pdb=" O SER F 79 " (cutoff:3.500A) 939 hydrogen bonds defined for protein. 2583 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: 3.74 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6002 1.34 - 1.45: 2956 1.45 - 1.57: 11136 1.57 - 1.69: 46 1.69 - 1.81: 256 Bond restraints: 20396 Sorted by residual: bond pdb=" N GLN E 210 " pdb=" CA GLN E 210 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.27e+00 bond pdb=" N GLN B 210 " pdb=" CA GLN B 210 " ideal model delta sigma weight residual 1.458 1.483 -0.025 1.90e-02 2.77e+03 1.76e+00 bond pdb=" C HIS D 297 " pdb=" N GLU D 298 " ideal model delta sigma weight residual 1.328 1.339 -0.011 1.30e-02 5.92e+03 7.56e-01 bond pdb=" CA GLU A 298 " pdb=" CB GLU A 298 " ideal model delta sigma weight residual 1.527 1.541 -0.014 1.61e-02 3.86e+03 7.53e-01 bond pdb=" CA GLU D 298 " pdb=" CB GLU D 298 " ideal model delta sigma weight residual 1.527 1.541 -0.014 1.61e-02 3.86e+03 7.44e-01 ... (remaining 20391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 26986 0.95 - 1.90: 505 1.90 - 2.85: 112 2.85 - 3.80: 53 3.80 - 4.75: 18 Bond angle restraints: 27674 Sorted by residual: angle pdb=" N GLY A 555 " pdb=" CA GLY A 555 " pdb=" C GLY A 555 " ideal model delta sigma weight residual 111.21 113.83 -2.62 1.04e+00 9.25e-01 6.35e+00 angle pdb=" N GLY D 555 " pdb=" CA GLY D 555 " pdb=" C GLY D 555 " ideal model delta sigma weight residual 111.21 113.81 -2.60 1.04e+00 9.25e-01 6.25e+00 angle pdb=" C SER B 443 " pdb=" N SER B 444 " pdb=" CA SER B 444 " ideal model delta sigma weight residual 121.54 126.16 -4.62 1.91e+00 2.74e-01 5.85e+00 angle pdb=" C SER E 443 " pdb=" N SER E 444 " pdb=" CA SER E 444 " ideal model delta sigma weight residual 121.54 126.14 -4.60 1.91e+00 2.74e-01 5.80e+00 angle pdb=" CA GLU A 298 " pdb=" CB GLU A 298 " pdb=" CG GLU A 298 " ideal model delta sigma weight residual 114.10 118.08 -3.98 2.00e+00 2.50e-01 3.95e+00 ... (remaining 27669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 11134 18.01 - 36.01: 994 36.01 - 54.02: 205 54.02 - 72.03: 41 72.03 - 90.03: 12 Dihedral angle restraints: 12386 sinusoidal: 5334 harmonic: 7052 Sorted by residual: dihedral pdb=" CA ASN E 153 " pdb=" C ASN E 153 " pdb=" N GLY E 154 " pdb=" CA GLY E 154 " ideal model delta harmonic sigma weight residual -180.00 -160.60 -19.40 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA ASN B 153 " pdb=" C ASN B 153 " pdb=" N GLY B 154 " pdb=" CA GLY B 154 " ideal model delta harmonic sigma weight residual -180.00 -160.61 -19.39 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA ASP E 398 " pdb=" CB ASP E 398 " pdb=" CG ASP E 398 " pdb=" OD1 ASP E 398 " ideal model delta sinusoidal sigma weight residual -30.00 -89.40 59.40 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 12383 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1865 0.025 - 0.051: 735 0.051 - 0.076: 272 0.076 - 0.102: 110 0.102 - 0.127: 54 Chirality restraints: 3036 Sorted by residual: chirality pdb=" CA ILE B 606 " pdb=" N ILE B 606 " pdb=" C ILE B 606 " pdb=" CB ILE B 606 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 chirality pdb=" CA ILE E 606 " pdb=" N ILE E 606 " pdb=" C ILE E 606 " pdb=" CB ILE E 606 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA ILE A 504 " pdb=" N ILE A 504 " pdb=" C ILE A 504 " pdb=" CB ILE A 504 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 3033 not shown) Planarity restraints: 3476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 314 " -0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO B 315 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 315 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 315 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN E 314 " 0.021 5.00e-02 4.00e+02 3.14e-02 1.58e+00 pdb=" N PRO E 315 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO E 315 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 315 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 624 " -0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO D 625 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO D 625 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 625 " -0.017 5.00e-02 4.00e+02 ... (remaining 3473 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 769 2.72 - 3.27: 19449 3.27 - 3.81: 32830 3.81 - 4.36: 39606 4.36 - 4.90: 68529 Nonbonded interactions: 161183 Sorted by model distance: nonbonded pdb=" OG SER E 160 " pdb=" OD2 ASP E 165 " model vdw 2.178 3.040 nonbonded pdb=" OG SER B 160 " pdb=" OD2 ASP B 165 " model vdw 2.179 3.040 nonbonded pdb=" O ILE B 113 " pdb=" OG1 THR B 117 " model vdw 2.180 3.040 nonbonded pdb=" O ILE E 113 " pdb=" OG1 THR E 117 " model vdw 2.180 3.040 nonbonded pdb=" NE2 GLN A 392 " pdb=" OD1 ASN B 382 " model vdw 2.246 3.120 ... (remaining 161178 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' selection = chain 'D' } ncs_group { reference = (chain 'B' and resid 1 through 670) selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'U' selection = chain 'V' } 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: 7.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.620 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 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 : 0.002 0.032 20396 Z= 0.078 Angle : 0.388 4.745 27674 Z= 0.205 Chirality : 0.036 0.127 3036 Planarity : 0.003 0.032 3476 Dihedral : 14.055 90.032 7822 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.80 (0.18), residues: 2402 helix: 1.86 (0.17), residues: 1074 sheet: 0.15 (0.33), residues: 242 loop : -0.73 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 287 TYR 0.007 0.001 TYR B 555 PHE 0.007 0.001 PHE E 490 TRP 0.007 0.001 TRP A 577 HIS 0.001 0.000 HIS E 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00155 / 0.08 (20396) covalent geometry : angle 0.38797 / 0.20 (27674) hydrogen bonds : bond 0.15035 / 10.36 ( 931) hydrogen bonds : angle 5.38664 / 3.77 ( 2583) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 ASN cc_start: 0.8777 (m-40) cc_final: 0.8267 (m-40) REVERT: A 374 MET cc_start: 0.8925 (tpp) cc_final: 0.8599 (tpp) REVERT: B 120 ASP cc_start: 0.8658 (m-30) cc_final: 0.8174 (p0) REVERT: B 148 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8742 (mm-30) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.1903 time to fit residues: 70.3881 Evaluate side-chains 184 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.0170 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 235 optimal weight: 3.9990 overall best weight: 1.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 GLN A 713 HIS B 136 ASN B 425 ASN B 428 GLN D 590 GLN E 425 ASN E 428 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.050108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.039744 restraints weight = 101761.239| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.85 r_work: 0.2789 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20396 Z= 0.142 Angle : 0.503 6.492 27674 Z= 0.258 Chirality : 0.039 0.151 3036 Planarity : 0.003 0.038 3476 Dihedral : 5.265 74.368 2908 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.98 % Allowed : 10.16 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.90 (0.18), residues: 2402 helix: 1.97 (0.17), residues: 1082 sheet: 0.17 (0.33), residues: 232 loop : -0.72 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 88 TYR 0.010 0.001 TYR E 555 PHE 0.019 0.001 PHE D 381 TRP 0.012 0.001 TRP D 577 HIS 0.004 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (20396) covalent geometry : angle 0.50273 / 0.26 (27674) hydrogen bonds : bond 0.04254 / 2.85 ( 931) hydrogen bonds : angle 4.19193 / 2.94 ( 2583) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 MET cc_start: 0.9468 (tpp) cc_final: 0.9254 (tpp) REVERT: B 120 ASP cc_start: 0.9308 (m-30) cc_final: 0.8565 (p0) REVERT: C 61 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8821 (ptmm) REVERT: C 69 GLU cc_start: 0.8572 (tp30) cc_final: 0.8109 (tp30) REVERT: F 61 LYS cc_start: 0.9310 (pptt) cc_final: 0.9054 (pptt) REVERT: F 65 GLU cc_start: 0.8778 (mp0) cc_final: 0.8322 (mp0) outliers start: 21 outliers final: 9 residues processed: 196 average time/residue: 0.1586 time to fit residues: 47.2737 Evaluate side-chains 186 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 176 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 595 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 19 optimal weight: 0.0060 chunk 166 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 239 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 47 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.049269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.038870 restraints weight = 102819.735| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 3.88 r_work: 0.2761 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20396 Z= 0.148 Angle : 0.494 8.981 27674 Z= 0.252 Chirality : 0.038 0.148 3036 Planarity : 0.003 0.039 3476 Dihedral : 5.353 74.204 2908 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.35 % Allowed : 10.16 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.90 (0.18), residues: 2402 helix: 1.99 (0.17), residues: 1080 sheet: 0.12 (0.32), residues: 236 loop : -0.74 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 508 TYR 0.014 0.001 TYR F 111 PHE 0.011 0.001 PHE E 505 TRP 0.010 0.001 TRP D 577 HIS 0.007 0.001 HIS A 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (20396) covalent geometry : angle 0.49386 / 0.25 (27674) hydrogen bonds : bond 0.03980 / 2.67 ( 931) hydrogen bonds : angle 4.06158 / 2.87 ( 2583) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 MET cc_start: 0.9493 (tpp) cc_final: 0.9266 (tpp) REVERT: B 120 ASP cc_start: 0.9315 (m-30) cc_final: 0.8511 (p0) REVERT: C 50 MET cc_start: 0.9350 (mmm) cc_final: 0.9038 (mmt) REVERT: C 53 MET cc_start: 0.8842 (mmm) cc_final: 0.8641 (mmm) REVERT: C 61 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8909 (ptmm) REVERT: C 64 MET cc_start: 0.9515 (mtt) cc_final: 0.8981 (mmm) REVERT: C 69 GLU cc_start: 0.8702 (tp30) cc_final: 0.8135 (tp30) REVERT: E 348 MET cc_start: 0.8459 (mmm) cc_final: 0.7893 (mmm) outliers start: 29 outliers final: 13 residues processed: 204 average time/residue: 0.1538 time to fit residues: 47.9405 Evaluate side-chains 187 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 173 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain D residue 213 ARG Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 595 MET Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 477 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 153 optimal weight: 0.1980 chunk 104 optimal weight: 5.9990 chunk 182 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 170 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 211 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 ASN D 392 GLN E 47 HIS E 425 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.049445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.039161 restraints weight = 101906.314| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 3.85 r_work: 0.2771 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20396 Z= 0.111 Angle : 0.482 7.907 27674 Z= 0.243 Chirality : 0.038 0.143 3036 Planarity : 0.003 0.035 3476 Dihedral : 5.353 74.533 2908 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.68 % Allowed : 10.72 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.94 (0.18), residues: 2402 helix: 2.02 (0.17), residues: 1080 sheet: 0.08 (0.33), residues: 232 loop : -0.70 (0.19), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 508 TYR 0.041 0.001 TYR C 55 PHE 0.011 0.001 PHE B 251 TRP 0.009 0.001 TRP D 577 HIS 0.002 0.001 HIS D 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (20396) covalent geometry : angle 0.48162 / 0.24 (27674) hydrogen bonds : bond 0.03551 / 2.39 ( 931) hydrogen bonds : angle 3.90416 / 2.76 ( 2583) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8608 (tpt) cc_final: 0.8146 (tpt) REVERT: B 120 ASP cc_start: 0.9325 (m-30) cc_final: 0.8527 (p0) REVERT: B 227 MET cc_start: 0.8623 (pmm) cc_final: 0.8345 (pmm) REVERT: C 45 LEU cc_start: 0.9677 (mm) cc_final: 0.9476 (tp) REVERT: C 50 MET cc_start: 0.9353 (mmm) cc_final: 0.8956 (mmt) REVERT: C 61 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8957 (ptmm) REVERT: C 69 GLU cc_start: 0.8692 (tp30) cc_final: 0.8117 (tp30) REVERT: D 248 GLN cc_start: 0.9353 (mt0) cc_final: 0.9153 (mt0) REVERT: E 507 MET cc_start: 0.6264 (pmm) cc_final: 0.5448 (pmm) REVERT: F 50 MET cc_start: 0.9473 (mmm) cc_final: 0.8962 (mpp) outliers start: 36 outliers final: 21 residues processed: 200 average time/residue: 0.1430 time to fit residues: 44.1995 Evaluate side-chains 196 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain D residue 213 ARG Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 595 MET Chi-restraints excluded: chain E residue 115 GLN Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 477 MET Chi-restraints excluded: chain E residue 632 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 201 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 40 optimal weight: 0.0270 chunk 55 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 chunk 51 optimal weight: 0.0060 chunk 32 optimal weight: 0.9990 chunk 167 optimal weight: 5.9990 chunk 239 optimal weight: 5.9990 overall best weight: 1.2060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 ASN E 425 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.049136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.038854 restraints weight = 101507.709| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 3.83 r_work: 0.2763 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20396 Z= 0.125 Angle : 0.484 8.338 27674 Z= 0.244 Chirality : 0.038 0.136 3036 Planarity : 0.003 0.035 3476 Dihedral : 5.380 74.495 2908 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.58 % Allowed : 11.28 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.97 (0.18), residues: 2402 helix: 2.04 (0.17), residues: 1082 sheet: 0.03 (0.32), residues: 232 loop : -0.66 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 508 TYR 0.046 0.001 TYR C 55 PHE 0.020 0.001 PHE B 166 TRP 0.008 0.001 TRP D 577 HIS 0.002 0.000 HIS D 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (20396) covalent geometry : angle 0.48351 / 0.24 (27674) hydrogen bonds : bond 0.03565 / 2.39 ( 931) hydrogen bonds : angle 3.86780 / 2.74 ( 2583) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ASP cc_start: 0.9330 (m-30) cc_final: 0.8515 (p0) REVERT: B 227 MET cc_start: 0.8600 (pmm) cc_final: 0.8305 (pmm) REVERT: C 50 MET cc_start: 0.9415 (mmm) cc_final: 0.8658 (mmt) REVERT: C 61 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8944 (ptmm) REVERT: C 69 GLU cc_start: 0.8752 (tp30) cc_final: 0.8127 (tp30) REVERT: D 590 GLN cc_start: 0.9263 (OUTLIER) cc_final: 0.8653 (tp40) REVERT: E 507 MET cc_start: 0.6166 (pmm) cc_final: 0.5330 (pmm) REVERT: F 47 MET cc_start: 0.9158 (tpp) cc_final: 0.8531 (tpt) REVERT: F 50 MET cc_start: 0.9533 (mmm) cc_final: 0.8939 (mmm) REVERT: F 51 MET cc_start: 0.8375 (mmm) cc_final: 0.7996 (mmm) REVERT: F 53 MET cc_start: 0.8757 (mpp) cc_final: 0.8087 (mpp) outliers start: 34 outliers final: 24 residues processed: 206 average time/residue: 0.1474 time to fit residues: 46.1935 Evaluate side-chains 200 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain D residue 213 ARG Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 590 GLN Chi-restraints excluded: chain D residue 595 MET Chi-restraints excluded: chain E residue 115 GLN Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 477 MET Chi-restraints excluded: chain E residue 632 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 150 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 210 optimal weight: 4.9990 chunk 188 optimal weight: 9.9990 chunk 238 optimal weight: 2.9990 chunk 113 optimal weight: 0.1980 chunk 190 optimal weight: 6.9990 chunk 223 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.048202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.037917 restraints weight = 101862.750| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.82 r_work: 0.2731 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20396 Z= 0.181 Angle : 0.519 9.131 27674 Z= 0.264 Chirality : 0.039 0.175 3036 Planarity : 0.003 0.035 3476 Dihedral : 5.464 73.986 2908 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.72 % Allowed : 11.65 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.96 (0.18), residues: 2402 helix: 2.05 (0.17), residues: 1080 sheet: -0.13 (0.32), residues: 236 loop : -0.64 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 135 TYR 0.042 0.001 TYR C 55 PHE 0.011 0.001 PHE B 505 TRP 0.009 0.001 TRP D 577 HIS 0.002 0.001 HIS E 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (20396) covalent geometry : angle 0.51881 / 0.26 (27674) hydrogen bonds : bond 0.03887 / 2.60 ( 931) hydrogen bonds : angle 3.96091 / 2.81 ( 2583) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ASP cc_start: 0.9355 (m-30) cc_final: 0.8538 (p0) REVERT: B 171 MET cc_start: 0.9171 (mmm) cc_final: 0.8918 (mmm) REVERT: B 227 MET cc_start: 0.8604 (pmm) cc_final: 0.8274 (pmm) REVERT: C 53 MET cc_start: 0.8159 (mpp) cc_final: 0.7915 (mpp) REVERT: C 61 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.9008 (ptmm) REVERT: C 69 GLU cc_start: 0.8698 (tp30) cc_final: 0.8057 (tp30) REVERT: D 590 GLN cc_start: 0.9254 (OUTLIER) cc_final: 0.8649 (tp40) REVERT: E 507 MET cc_start: 0.6169 (pmm) cc_final: 0.5324 (pmm) REVERT: F 41 LYS cc_start: 0.7864 (pttm) cc_final: 0.7568 (pttm) REVERT: F 47 MET cc_start: 0.9164 (tpp) cc_final: 0.8741 (tpt) outliers start: 37 outliers final: 23 residues processed: 199 average time/residue: 0.1407 time to fit residues: 43.8959 Evaluate side-chains 195 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 590 GLN Chi-restraints excluded: chain D residue 595 MET Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain E residue 115 GLN Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 477 MET Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain F residue 53 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 126 optimal weight: 5.9990 chunk 223 optimal weight: 0.6980 chunk 206 optimal weight: 0.4980 chunk 180 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 ASN ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN E 476 ASN F 42 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.048842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.038547 restraints weight = 102131.418| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.86 r_work: 0.2754 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20396 Z= 0.114 Angle : 0.511 12.301 27674 Z= 0.255 Chirality : 0.039 0.157 3036 Planarity : 0.003 0.035 3476 Dihedral : 5.449 74.437 2908 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.77 % Allowed : 12.16 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.97 (0.18), residues: 2402 helix: 2.02 (0.16), residues: 1080 sheet: -0.06 (0.32), residues: 236 loop : -0.61 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 508 TYR 0.027 0.001 TYR C 55 PHE 0.010 0.001 PHE B 505 TRP 0.009 0.001 TRP D 577 HIS 0.001 0.000 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (20396) covalent geometry : angle 0.51128 / 0.26 (27674) hydrogen bonds : bond 0.03511 / 2.35 ( 931) hydrogen bonds : angle 3.87053 / 2.75 ( 2583) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ASP cc_start: 0.9358 (m-30) cc_final: 0.8556 (p0) REVERT: B 227 MET cc_start: 0.8586 (pmm) cc_final: 0.8267 (pmm) REVERT: C 61 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.9000 (ptmm) REVERT: C 69 GLU cc_start: 0.8738 (tp30) cc_final: 0.8109 (tp30) REVERT: D 374 MET cc_start: 0.9447 (tpp) cc_final: 0.9112 (tpp) REVERT: D 590 GLN cc_start: 0.9230 (OUTLIER) cc_final: 0.8624 (tp40) REVERT: E 171 MET cc_start: 0.9252 (tpt) cc_final: 0.9003 (mmm) REVERT: E 348 MET cc_start: 0.8615 (mmm) cc_final: 0.8303 (mmm) REVERT: E 507 MET cc_start: 0.6153 (pmm) cc_final: 0.5295 (pmm) REVERT: F 41 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7596 (pttm) REVERT: F 47 MET cc_start: 0.9156 (tpp) cc_final: 0.8688 (tpt) REVERT: F 50 MET cc_start: 0.9521 (mmm) cc_final: 0.9060 (mmt) REVERT: F 51 MET cc_start: 0.8407 (mmm) cc_final: 0.8119 (mmm) REVERT: F 53 MET cc_start: 0.8822 (mpp) cc_final: 0.8536 (mpp) REVERT: F 88 ARG cc_start: 0.8724 (mmm-85) cc_final: 0.8522 (mmm-85) outliers start: 38 outliers final: 23 residues processed: 201 average time/residue: 0.1386 time to fit residues: 43.2626 Evaluate side-chains 198 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 590 GLN Chi-restraints excluded: chain D residue 595 MET Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 477 MET Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain F residue 41 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 198 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 231 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 89 optimal weight: 0.0980 chunk 25 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 590 GLN C 73 GLN ** E 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.049139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.038855 restraints weight = 101116.951| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 3.84 r_work: 0.2768 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20396 Z= 0.101 Angle : 0.522 14.832 27674 Z= 0.258 Chirality : 0.038 0.214 3036 Planarity : 0.003 0.035 3476 Dihedral : 5.435 74.838 2908 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.68 % Allowed : 12.67 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.18), residues: 2402 helix: 2.17 (0.16), residues: 1064 sheet: -0.05 (0.32), residues: 236 loop : -0.58 (0.19), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 135 TYR 0.021 0.001 TYR F 111 PHE 0.009 0.001 PHE B 505 TRP 0.018 0.001 TRP F 78 HIS 0.002 0.000 HIS D 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (20396) covalent geometry : angle 0.52238 / 0.26 (27674) hydrogen bonds : bond 0.03335 / 2.23 ( 931) hydrogen bonds : angle 3.81637 / 2.70 ( 2583) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 178 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ASP cc_start: 0.9353 (m-30) cc_final: 0.8565 (p0) REVERT: B 227 MET cc_start: 0.8580 (pmm) cc_final: 0.8252 (pmm) REVERT: C 69 GLU cc_start: 0.8746 (tp30) cc_final: 0.8088 (tp30) REVERT: D 211 MET cc_start: 0.9101 (mtp) cc_final: 0.8493 (mpp) REVERT: D 374 MET cc_start: 0.9446 (tpp) cc_final: 0.9094 (tpp) REVERT: D 590 GLN cc_start: 0.9209 (OUTLIER) cc_final: 0.8614 (tp40) REVERT: E 171 MET cc_start: 0.9269 (tpt) cc_final: 0.8732 (tpp) REVERT: F 41 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7568 (pttm) REVERT: F 47 MET cc_start: 0.9136 (tpp) cc_final: 0.8756 (tpt) REVERT: F 53 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8417 (mpp) outliers start: 36 outliers final: 22 residues processed: 200 average time/residue: 0.1443 time to fit residues: 44.5419 Evaluate side-chains 194 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 590 GLN Chi-restraints excluded: chain D residue 595 MET Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain F residue 41 LYS Chi-restraints excluded: chain F residue 53 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 236 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 231 optimal weight: 4.9990 chunk 75 optimal weight: 0.0270 chunk 51 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 159 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.048753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.038546 restraints weight = 101027.677| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 3.79 r_work: 0.2759 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20396 Z= 0.124 Angle : 0.549 14.354 27674 Z= 0.269 Chirality : 0.039 0.214 3036 Planarity : 0.003 0.035 3476 Dihedral : 5.485 74.806 2908 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.72 % Allowed : 12.67 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.06 (0.18), residues: 2402 helix: 2.15 (0.16), residues: 1064 sheet: -0.05 (0.32), residues: 236 loop : -0.57 (0.19), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 88 TYR 0.020 0.001 TYR F 111 PHE 0.008 0.001 PHE E 490 TRP 0.015 0.001 TRP F 78 HIS 0.002 0.000 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (20396) covalent geometry : angle 0.54864 / 0.27 (27674) hydrogen bonds : bond 0.03509 / 2.35 ( 931) hydrogen bonds : angle 3.85436 / 2.73 ( 2583) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ASP cc_start: 0.9352 (m-30) cc_final: 0.8519 (p0) REVERT: B 227 MET cc_start: 0.8613 (pmm) cc_final: 0.8280 (pmm) REVERT: C 69 GLU cc_start: 0.8743 (tp30) cc_final: 0.8066 (tp30) REVERT: D 211 MET cc_start: 0.9095 (mtp) cc_final: 0.8571 (mpp) REVERT: D 374 MET cc_start: 0.9457 (tpp) cc_final: 0.9105 (tpp) REVERT: D 590 GLN cc_start: 0.9224 (OUTLIER) cc_final: 0.8626 (tp40) REVERT: D 595 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8323 (mtp) REVERT: F 41 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7693 (pttm) REVERT: F 47 MET cc_start: 0.9141 (tpp) cc_final: 0.8773 (tpt) REVERT: F 53 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8424 (mpp) outliers start: 37 outliers final: 25 residues processed: 196 average time/residue: 0.1340 time to fit residues: 41.5022 Evaluate side-chains 197 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 590 GLN Chi-restraints excluded: chain D residue 595 MET Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 477 MET Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain F residue 41 LYS Chi-restraints excluded: chain F residue 53 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 52 optimal weight: 0.8980 chunk 123 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 197 optimal weight: 6.9990 chunk 186 optimal weight: 8.9990 chunk 184 optimal weight: 2.9990 chunk 189 optimal weight: 0.3980 chunk 164 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.048206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.037917 restraints weight = 102388.383| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 3.84 r_work: 0.2736 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20396 Z= 0.159 Angle : 0.576 16.307 27674 Z= 0.282 Chirality : 0.040 0.213 3036 Planarity : 0.003 0.035 3476 Dihedral : 5.556 74.709 2908 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.40 % Allowed : 12.91 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.18), residues: 2402 helix: 2.11 (0.16), residues: 1070 sheet: -0.09 (0.32), residues: 236 loop : -0.56 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 88 TYR 0.020 0.001 TYR F 111 PHE 0.011 0.001 PHE B 412 TRP 0.013 0.001 TRP F 78 HIS 0.002 0.000 HIS E 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (20396) covalent geometry : angle 0.57574 / 0.28 (27674) hydrogen bonds : bond 0.03722 / 2.50 ( 931) hydrogen bonds : angle 3.94246 / 2.78 ( 2583) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 MET cc_start: 0.8604 (pmm) cc_final: 0.8257 (pmm) REVERT: C 69 GLU cc_start: 0.8756 (tp30) cc_final: 0.8089 (tp30) REVERT: D 211 MET cc_start: 0.9074 (mtp) cc_final: 0.8587 (mpp) REVERT: D 248 GLN cc_start: 0.9511 (mt0) cc_final: 0.9231 (mp10) REVERT: D 590 GLN cc_start: 0.9227 (OUTLIER) cc_final: 0.8617 (tp40) REVERT: D 595 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8342 (mtp) REVERT: F 41 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7768 (pttm) REVERT: F 47 MET cc_start: 0.9163 (tpp) cc_final: 0.8808 (tpt) REVERT: F 64 MET cc_start: 0.9459 (mtt) cc_final: 0.9197 (mmm) outliers start: 30 outliers final: 22 residues processed: 191 average time/residue: 0.1301 time to fit residues: 39.2754 Evaluate side-chains 194 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 590 GLN Chi-restraints excluded: chain D residue 595 MET Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain F residue 41 LYS Chi-restraints excluded: chain F residue 53 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 133 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 235 optimal weight: 2.9990 chunk 197 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 224 optimal weight: 0.8980 chunk 161 optimal weight: 0.5980 chunk 6 optimal weight: 0.0970 chunk 207 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 476 ASN ** E 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.048769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.038540 restraints weight = 101902.216| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 3.83 r_work: 0.2760 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20396 Z= 0.112 Angle : 0.560 14.706 27674 Z= 0.273 Chirality : 0.039 0.213 3036 Planarity : 0.003 0.035 3476 Dihedral : 5.538 75.202 2908 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.16 % Allowed : 13.28 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.18), residues: 2402 helix: 2.15 (0.16), residues: 1068 sheet: -0.08 (0.32), residues: 236 loop : -0.57 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 88 TYR 0.019 0.001 TYR F 111 PHE 0.012 0.001 PHE B 251 TRP 0.009 0.001 TRP D 577 HIS 0.002 0.000 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (20396) covalent geometry : angle 0.56022 / 0.27 (27674) hydrogen bonds : bond 0.03417 / 2.30 ( 931) hydrogen bonds : angle 3.86333 / 2.73 ( 2583) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4240.35 seconds wall clock time: 73 minutes 51.01 seconds (4431.01 seconds total)