Starting phenix.real_space_refine on Sat Sep 28 20:01:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpl_14857/09_2024/7zpl_14857.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpl_14857/09_2024/7zpl_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpl_14857/09_2024/7zpl_14857.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpl_14857/09_2024/7zpl_14857.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpl_14857/09_2024/7zpl_14857.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpl_14857/09_2024/7zpl_14857.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 13.00, per 1000 atoms: 0.65 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: 4.82 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 2.34 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: 7.67 Time building geometry restraints manager: 5.72 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: 11152 18.01 - 36.01: 1002 36.01 - 54.02: 211 54.02 - 72.03: 67 72.03 - 90.03: 14 Dihedral angle restraints: 12446 sinusoidal: 5394 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 12443 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: 4.220 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: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 47.260 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 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= 0.099 Angle : 0.388 4.745 27674 Z= 0.205 Chirality : 0.036 0.127 3036 Planarity : 0.003 0.032 3476 Dihedral : 14.558 90.032 7882 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (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 TRP 0.007 0.001 TRP A 577 HIS 0.001 0.000 HIS E 32 PHE 0.007 0.001 PHE E 490 TYR 0.007 0.001 TYR B 555 ARG 0.002 0.000 ARG E 287 *********************** 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 fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 2.252 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: 0.8266 (m-40) REVERT: A 374 MET cc_start: 0.8924 (tpp) cc_final: 0.8597 (tpp) REVERT: B 120 ASP cc_start: 0.8657 (m-30) cc_final: 0.8174 (p0) REVERT: B 148 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8742 (mm-30) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.4077 time to fit residues: 149.8797 Evaluate side-chains 184 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 2.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.7980 chunk 181 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 62 optimal weight: 0.0270 chunk 122 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 188 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 140 optimal weight: 0.8980 chunk 217 optimal weight: 4.9990 overall best weight: 0.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20396 Z= 0.150 Angle : 0.489 6.784 27674 Z= 0.250 Chirality : 0.038 0.196 3036 Planarity : 0.003 0.038 3476 Dihedral : 8.171 74.657 2968 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.12 % Allowed : 9.93 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.18), residues: 2402 helix: 1.96 (0.17), residues: 1080 sheet: 0.16 (0.33), residues: 234 loop : -0.70 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 577 HIS 0.005 0.001 HIS A 510 PHE 0.019 0.001 PHE D 381 TYR 0.009 0.001 TYR E 555 ARG 0.006 0.000 ARG F 88 *********************** 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 210 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 186 time to evaluate : 2.620 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: B 120 ASP cc_start: 0.8704 (m-30) cc_final: 0.8256 (p0) REVERT: B 256 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7946 (mm-30) REVERT: F 65 GLU cc_start: 0.8125 (mp0) cc_final: 0.7830 (mp0) outliers start: 24 outliers final: 11 residues processed: 199 average time/residue: 0.3613 time to fit residues: 109.5474 Evaluate side-chains 188 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 177 time to evaluate : 2.443 ------------------------------------------------------------------------------- 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 115 GLN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain C residue 105 THR 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 121 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 181 optimal weight: 0.9980 chunk 148 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 235 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 chunk 216 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 HIS ** D 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1735 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= 0.264 Angle : 0.513 8.836 27674 Z= 0.262 Chirality : 0.039 0.144 3036 Planarity : 0.004 0.066 3476 Dihedral : 8.267 73.949 2968 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.54 % Allowed : 10.34 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.18), residues: 2402 helix: 1.97 (0.17), residues: 1082 sheet: 0.05 (0.32), residues: 236 loop : -0.71 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 577 HIS 0.012 0.001 HIS A 713 PHE 0.016 0.001 PHE B 166 TYR 0.011 0.001 TYR E 555 ARG 0.007 0.000 ARG D 508 *********************** 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 216 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 183 time to evaluate : 2.388 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: 0.8720 (m-30) cc_final: 0.8196 (p0) REVERT: C 50 MET cc_start: 0.8828 (mmm) cc_final: 0.8410 (mmt) outliers start: 33 outliers final: 16 residues processed: 204 average time/residue: 0.3348 time to fit residues: 104.3070 Evaluate side-chains 187 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 171 time to evaluate : 2.205 ------------------------------------------------------------------------------- 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 156 THR Chi-restraints excluded: chain B residue 307 THR 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 523 MET 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 632 VAL Chi-restraints excluded: chain F residue 41 LYS Chi-restraints excluded: chain F residue 66 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 146 optimal weight: 0.7980 chunk 219 optimal weight: 5.9990 chunk 231 optimal weight: 5.9990 chunk 114 optimal weight: 0.0030 chunk 207 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 GLN B 425 ASN D 392 GLN E 47 HIS E 382 ASN E 425 ASN E 476 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20396 Z= 0.171 Angle : 0.485 7.875 27674 Z= 0.246 Chirality : 0.038 0.150 3036 Planarity : 0.003 0.036 3476 Dihedral : 8.249 74.519 2968 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.72 % Allowed : 10.81 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.18), residues: 2402 helix: 2.00 (0.16), residues: 1082 sheet: 0.03 (0.32), residues: 232 loop : -0.68 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 577 HIS 0.002 0.001 HIS E 47 PHE 0.010 0.001 PHE B 505 TYR 0.045 0.001 TYR C 55 ARG 0.007 0.000 ARG A 716 *********************** 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 217 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 180 time to evaluate : 2.537 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 1 MET cc_start: 0.8608 (tpt) cc_final: 0.8302 (tpt) REVERT: B 120 ASP cc_start: 0.8742 (m-30) cc_final: 0.8214 (p0) REVERT: C 50 MET cc_start: 0.8840 (mmm) cc_final: 0.8375 (mmt) REVERT: E 507 MET cc_start: 0.6432 (pmm) cc_final: 0.5667 (pmm) REVERT: F 46 ARG cc_start: 0.8375 (ttm110) cc_final: 0.7705 (ttm-80) REVERT: F 47 MET cc_start: 0.8966 (tpp) cc_final: 0.8669 (tpt) REVERT: F 50 MET cc_start: 0.8878 (mmm) cc_final: 0.8517 (mpp) outliers start: 37 outliers final: 19 residues processed: 203 average time/residue: 0.3405 time to fit residues: 105.6623 Evaluate side-chains 194 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 175 time to evaluate : 2.428 ------------------------------------------------------------------------------- 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 618 THR 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 456 THR Chi-restraints excluded: chain D residue 485 MET 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 307 THR Chi-restraints excluded: chain E residue 409 MET Chi-restraints excluded: chain E residue 477 MET Chi-restraints excluded: chain F residue 66 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 160 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 208 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20396 Z= 0.244 Angle : 0.510 8.421 27674 Z= 0.260 Chirality : 0.039 0.154 3036 Planarity : 0.003 0.035 3476 Dihedral : 8.294 74.087 2968 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.54 % Allowed : 11.65 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.18), residues: 2402 helix: 2.08 (0.16), residues: 1068 sheet: -0.12 (0.32), residues: 240 loop : -0.60 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 577 HIS 0.002 0.001 HIS E 32 PHE 0.011 0.001 PHE B 505 TYR 0.047 0.001 TYR C 55 ARG 0.005 0.000 ARG D 508 *********************** 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 213 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 180 time to evaluate : 2.237 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: 0.8787 (m-30) cc_final: 0.8242 (p0) REVERT: C 50 MET cc_start: 0.8892 (mmm) cc_final: 0.8162 (mmt) REVERT: D 590 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8790 (tp40) REVERT: E 348 MET cc_start: 0.8127 (mmm) cc_final: 0.7842 (mmm) REVERT: E 507 MET cc_start: 0.6377 (pmm) cc_final: 0.5516 (pmm) REVERT: F 50 MET cc_start: 0.8989 (mmm) cc_final: 0.8622 (mmm) REVERT: F 53 MET cc_start: 0.8652 (mpp) cc_final: 0.8150 (mpp) outliers start: 33 outliers final: 24 residues processed: 198 average time/residue: 0.3376 time to fit residues: 102.2560 Evaluate side-chains 194 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 169 time to evaluate : 2.291 ------------------------------------------------------------------------------- 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 156 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 409 MET 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 485 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 409 MET Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain F residue 66 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 8.9990 chunk 208 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 232 optimal weight: 0.8980 chunk 192 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 20396 Z= 0.296 Angle : 0.537 8.714 27674 Z= 0.275 Chirality : 0.040 0.138 3036 Planarity : 0.003 0.035 3476 Dihedral : 8.345 73.928 2968 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.91 % Allowed : 11.65 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.18), residues: 2402 helix: 2.05 (0.16), residues: 1062 sheet: -0.20 (0.32), residues: 236 loop : -0.65 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 438 HIS 0.003 0.001 HIS E 32 PHE 0.013 0.001 PHE B 505 TYR 0.040 0.001 TYR C 55 ARG 0.004 0.000 ARG D 508 *********************** 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 217 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 176 time to evaluate : 2.227 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: B 171 MET cc_start: 0.8954 (mmm) cc_final: 0.8638 (mmm) REVERT: B 477 MET cc_start: 0.8239 (ppp) cc_final: 0.7928 (ptm) REVERT: D 590 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8789 (tp40) REVERT: E 171 MET cc_start: 0.8754 (tpt) cc_final: 0.8443 (mmm) REVERT: E 507 MET cc_start: 0.6423 (pmm) cc_final: 0.5585 (pmm) REVERT: F 47 MET cc_start: 0.9004 (tpp) cc_final: 0.8608 (tpt) REVERT: F 50 MET cc_start: 0.8935 (mmm) cc_final: 0.8580 (mmm) outliers start: 41 outliers final: 27 residues processed: 203 average time/residue: 0.3239 time to fit residues: 101.3719 Evaluate side-chains 198 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 170 time to evaluate : 2.426 ------------------------------------------------------------------------------- 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 264 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 409 MET 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 485 MET Chi-restraints excluded: chain D residue 557 VAL 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 227 MET Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 409 MET Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain F residue 66 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 132 optimal weight: 0.0020 chunk 169 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 231 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN E 425 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2314 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= 0.156 Angle : 0.511 10.287 27674 Z= 0.257 Chirality : 0.038 0.149 3036 Planarity : 0.003 0.036 3476 Dihedral : 8.304 74.876 2968 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.91 % Allowed : 12.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.18), residues: 2402 helix: 2.11 (0.17), residues: 1064 sheet: -0.14 (0.31), residues: 240 loop : -0.62 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 78 HIS 0.001 0.000 HIS D 510 PHE 0.011 0.001 PHE B 505 TYR 0.023 0.001 TYR C 55 ARG 0.005 0.000 ARG F 46 *********************** 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 219 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 178 time to evaluate : 2.446 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: B 477 MET cc_start: 0.8252 (ppp) cc_final: 0.7895 (ptm) REVERT: D 374 MET cc_start: 0.9252 (tpp) cc_final: 0.8933 (tpp) REVERT: D 590 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8756 (tp40) REVERT: F 50 MET cc_start: 0.8876 (mmm) cc_final: 0.8583 (mmm) outliers start: 41 outliers final: 24 residues processed: 202 average time/residue: 0.3346 time to fit residues: 103.0404 Evaluate side-chains 194 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 169 time to evaluate : 2.320 ------------------------------------------------------------------------------- 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 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 409 MET Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain D residue 450 VAL 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 53 MET Chi-restraints excluded: chain F residue 66 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 69 optimal weight: 0.4980 chunk 45 optimal weight: 0.0970 chunk 44 optimal weight: 0.0970 chunk 147 optimal weight: 6.9990 chunk 157 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2353 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= 0.129 Angle : 0.518 10.896 27674 Z= 0.257 Chirality : 0.038 0.149 3036 Planarity : 0.003 0.036 3476 Dihedral : 8.263 75.315 2968 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.58 % Allowed : 12.58 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.18), residues: 2402 helix: 2.15 (0.17), residues: 1062 sheet: -0.11 (0.31), residues: 240 loop : -0.60 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 577 HIS 0.001 0.000 HIS A 510 PHE 0.009 0.001 PHE B 505 TYR 0.019 0.001 TYR E 557 ARG 0.006 0.000 ARG F 46 *********************** 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 210 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 176 time to evaluate : 2.351 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: B 148 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8826 (mm-30) REVERT: B 477 MET cc_start: 0.8259 (ppp) cc_final: 0.7881 (ptm) REVERT: D 590 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8744 (tp40) REVERT: E 171 MET cc_start: 0.8853 (mmm) cc_final: 0.8548 (mmm) REVERT: F 47 MET cc_start: 0.8825 (tpp) cc_final: 0.8537 (tpt) outliers start: 34 outliers final: 25 residues processed: 198 average time/residue: 0.3244 time to fit residues: 98.7612 Evaluate side-chains 195 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 169 time to evaluate : 2.265 ------------------------------------------------------------------------------- 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 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 C residue 61 LYS 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 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 477 MET Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain F residue 53 MET Chi-restraints excluded: chain F residue 66 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 5.9990 chunk 221 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 194 optimal weight: 0.9980 chunk 203 optimal weight: 0.6980 chunk 214 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20396 Z= 0.160 Angle : 0.530 11.345 27674 Z= 0.263 Chirality : 0.039 0.161 3036 Planarity : 0.003 0.036 3476 Dihedral : 8.279 75.203 2968 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.35 % Allowed : 12.86 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.18), residues: 2402 helix: 2.18 (0.16), residues: 1064 sheet: -0.14 (0.32), residues: 236 loop : -0.57 (0.19), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 577 HIS 0.002 0.000 HIS A 510 PHE 0.008 0.001 PHE E 490 TYR 0.022 0.001 TYR E 557 ARG 0.005 0.000 ARG F 46 *********************** 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 200 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 171 time to evaluate : 2.315 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: 0.8789 (m-30) cc_final: 0.8233 (p0) REVERT: B 148 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8813 (mm-30) REVERT: C 53 MET cc_start: 0.8454 (ppp) cc_final: 0.8164 (pmm) REVERT: D 211 MET cc_start: 0.8705 (mtp) cc_final: 0.8476 (mpp) REVERT: D 590 GLN cc_start: 0.9107 (OUTLIER) cc_final: 0.8725 (tp40) REVERT: D 595 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8105 (mtp) REVERT: F 45 LEU cc_start: 0.9277 (mm) cc_final: 0.9066 (mm) REVERT: F 50 MET cc_start: 0.8945 (mmm) cc_final: 0.8726 (mmt) outliers start: 29 outliers final: 24 residues processed: 190 average time/residue: 0.3220 time to fit residues: 95.7325 Evaluate side-chains 194 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 168 time to evaluate : 2.297 ------------------------------------------------------------------------------- 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 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 C residue 61 LYS 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 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 477 MET Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain F residue 53 MET Chi-restraints excluded: chain F residue 66 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 3.9990 chunk 227 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 239 optimal weight: 4.9990 chunk 220 optimal weight: 1.9990 chunk 190 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 248 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20396 Z= 0.266 Angle : 0.603 15.517 27674 Z= 0.295 Chirality : 0.040 0.203 3036 Planarity : 0.003 0.039 3476 Dihedral : 8.378 74.581 2968 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.21 % Allowed : 13.23 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.18), residues: 2402 helix: 2.05 (0.16), residues: 1078 sheet: -0.15 (0.32), residues: 236 loop : -0.67 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 438 HIS 0.003 0.001 HIS E 32 PHE 0.010 0.001 PHE B 505 TYR 0.023 0.001 TYR E 557 ARG 0.005 0.000 ARG F 46 ********************** 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 194 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 168 time to evaluate : 2.385 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: B 477 MET cc_start: 0.8321 (ppp) cc_final: 0.7930 (ptm) REVERT: D 211 MET cc_start: 0.8709 (mtp) cc_final: 0.8479 (mpp) REVERT: D 590 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8760 (tp40) REVERT: D 595 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8181 (mtp) REVERT: F 45 LEU cc_start: 0.9281 (mm) cc_final: 0.9073 (mm) REVERT: F 50 MET cc_start: 0.8967 (mmm) cc_final: 0.8736 (mmt) outliers start: 26 outliers final: 20 residues processed: 186 average time/residue: 0.3208 time to fit residues: 92.7478 Evaluate side-chains 188 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 166 time to evaluate : 2.259 ------------------------------------------------------------------------------- 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 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 51 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 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 53 MET Chi-restraints excluded: chain F residue 66 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 1.9990 chunk 202 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 175 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 195 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 248 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.048416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.038171 restraints weight = 101453.156| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 3.82 r_work: 0.2748 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20396 Z= 0.181 Angle : 0.578 14.934 27674 Z= 0.282 Chirality : 0.039 0.212 3036 Planarity : 0.003 0.046 3476 Dihedral : 8.345 75.163 2968 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.21 % Allowed : 13.47 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.18), residues: 2402 helix: 2.15 (0.16), residues: 1068 sheet: -0.02 (0.32), residues: 232 loop : -0.63 (0.19), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 577 HIS 0.002 0.000 HIS A 510 PHE 0.011 0.001 PHE B 251 TYR 0.022 0.001 TYR E 557 ARG 0.005 0.000 ARG F 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3898.27 seconds wall clock time: 71 minutes 5.33 seconds (4265.33 seconds total)