Starting phenix.real_space_refine on Fri Aug 7 00:44:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hwg_35057/08_2026/8hwg_35057.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hwg_35057/08_2026/8hwg_35057.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hwg_35057/08_2026/8hwg_35057.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hwg_35057/08_2026/8hwg_35057.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8hwg_35057/08_2026/8hwg_35057.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hwg_35057/08_2026/8hwg_35057.cif" model { file = "/net/cci-nas-00/data/ceres_data/8hwg_35057/08_2026/8hwg_35057.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hwg_35057/08_2026/8hwg_35057.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 22 5.49 5 Mg 6 5.21 5 S 98 5.16 5 C 11445 2.51 5 N 3085 2.21 5 O 3454 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18110 Number of models: 1 Model: "" Number of chains: 13 Chain: "C" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2996 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 18, 'TRANS': 353} Chain: "B" Number of atoms: 2972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2972 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 17, 'TRANS': 351} Chain: "D" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3051 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 18, 'TRANS': 359} Chain: "A" Number of atoms: 2972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2972 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 17, 'TRANS': 351} Chain: "F" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2843 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 14, 'TRANS': 337} Chain breaks: 1 Chain: "E" Number of atoms: 2972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2972 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 17, 'TRANS': 351} Chain: "S" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.92, per 1000 atoms: 0.22 Number of scatterers: 18110 At special positions: 0 Unit cell: (125.925, 131.4, 120.45, 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 98 16.00 P 22 15.00 Mg 6 11.99 O 3454 8.00 N 3085 7.00 C 11445 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: 1.17 Conformation dependent library (CDL) restraints added in 823.2 milliseconds 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4204 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 26 sheets defined 41.5% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'C' and resid 324 through 334 removed outlier: 3.618A pdb=" N ALA C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 371 removed outlier: 3.952A pdb=" N LEU C 367 " --> pdb=" O LEU C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 375 Processing helix chain 'C' and resid 376 through 381 removed outlier: 3.781A pdb=" N SER C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 384 No H-bonds generated for 'chain 'C' and resid 382 through 384' Processing helix chain 'C' and resid 385 through 400 removed outlier: 3.864A pdb=" N LYS C 390 " --> pdb=" O PRO C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 435 removed outlier: 3.573A pdb=" N ASP C 432 " --> pdb=" O SER C 429 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS C 435 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 469 Processing helix chain 'C' and resid 476 through 489 Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 529 through 534 removed outlier: 3.572A pdb=" N THR C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 570 through 577 Processing helix chain 'C' and resid 635 through 642 removed outlier: 3.728A pdb=" N ALA C 639 " --> pdb=" O GLY C 635 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU C 640 " --> pdb=" O ARG C 636 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN C 642 " --> pdb=" O ALA C 638 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 635 through 642' Processing helix chain 'C' and resid 654 through 661 removed outlier: 3.738A pdb=" N LYS C 658 " --> pdb=" O GLY C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 680 removed outlier: 3.555A pdb=" N LEU C 669 " --> pdb=" O ARG C 665 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS C 678 " --> pdb=" O LYS C 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 337 removed outlier: 3.515A pdb=" N ASN B 328 " --> pdb=" O ASN B 324 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN B 337 " --> pdb=" O ILE B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 371 removed outlier: 3.752A pdb=" N LEU B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 375 Processing helix chain 'B' and resid 376 through 381 removed outlier: 3.584A pdb=" N SER B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 385 through 400 removed outlier: 3.731A pdb=" N LYS B 390 " --> pdb=" O PRO B 386 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR B 391 " --> pdb=" O ARG B 387 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.863A pdb=" N LYS B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 469 Processing helix chain 'B' and resid 475 through 488 removed outlier: 3.548A pdb=" N ARG B 479 " --> pdb=" O ASN B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 491 No H-bonds generated for 'chain 'B' and resid 489 through 491' Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 528 through 532 removed outlier: 3.759A pdb=" N ILE B 531 " --> pdb=" O GLY B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 577 removed outlier: 3.575A pdb=" N ILE B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 619 removed outlier: 3.705A pdb=" N ARG B 619 " --> pdb=" O ASN B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 640 Processing helix chain 'B' and resid 654 through 661 Processing helix chain 'B' and resid 664 through 680 removed outlier: 3.584A pdb=" N PHE B 668 " --> pdb=" O TYR B 664 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS B 678 " --> pdb=" O LYS B 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 335 removed outlier: 3.614A pdb=" N ASN D 328 " --> pdb=" O ASN D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 371 Processing helix chain 'D' and resid 372 through 375 Processing helix chain 'D' and resid 376 through 381 Processing helix chain 'D' and resid 382 through 385 removed outlier: 3.586A pdb=" N CYS D 385 " --> pdb=" O GLU D 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 382 through 385' Processing helix chain 'D' and resid 387 through 400 removed outlier: 3.845A pdb=" N THR D 391 " --> pdb=" O ARG D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 433 removed outlier: 3.545A pdb=" N ALA D 433 " --> pdb=" O GLY D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 469 Processing helix chain 'D' and resid 472 through 474 No H-bonds generated for 'chain 'D' and resid 472 through 474' Processing helix chain 'D' and resid 475 through 489 removed outlier: 3.693A pdb=" N ARG D 479 " --> pdb=" O ASN D 475 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N CYS D 489 " --> pdb=" O THR D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 521 Processing helix chain 'D' and resid 541 through 546 Processing helix chain 'D' and resid 570 through 577 Processing helix chain 'D' and resid 614 through 619 removed outlier: 3.610A pdb=" N ARG D 619 " --> pdb=" O ASN D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 641 Processing helix chain 'D' and resid 656 through 661 removed outlier: 4.228A pdb=" N GLN D 660 " --> pdb=" O ASP D 656 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN D 661 " --> pdb=" O GLY D 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 656 through 661' Processing helix chain 'D' and resid 664 through 680 Processing helix chain 'D' and resid 689 through 692 removed outlier: 3.713A pdb=" N GLU D 692 " --> pdb=" O THR D 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 689 through 692' Processing helix chain 'D' and resid 693 through 700 Processing helix chain 'A' and resid 324 through 334 removed outlier: 3.535A pdb=" N ALA A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 371 Processing helix chain 'A' and resid 376 through 381 Processing helix chain 'A' and resid 382 through 385 removed outlier: 3.630A pdb=" N CYS A 385 " --> pdb=" O GLU A 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 382 through 385' Processing helix chain 'A' and resid 387 through 400 Processing helix chain 'A' and resid 429 through 433 Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 476 through 488 removed outlier: 3.858A pdb=" N LEU A 481 " --> pdb=" O LYS A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 570 through 577 removed outlier: 3.651A pdb=" N ILE A 574 " --> pdb=" O ARG A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 619 Processing helix chain 'A' and resid 632 through 634 No H-bonds generated for 'chain 'A' and resid 632 through 634' Processing helix chain 'A' and resid 635 through 640 removed outlier: 3.790A pdb=" N ALA A 639 " --> pdb=" O GLY A 635 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU A 640 " --> pdb=" O ARG A 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 635 through 640' Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 664 through 680 removed outlier: 3.985A pdb=" N LYS A 678 " --> pdb=" O LYS A 674 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR A 679 " --> pdb=" O TRP A 675 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 336 removed outlier: 3.766A pdb=" N THR F 336 " --> pdb=" O ARG F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 371 removed outlier: 3.677A pdb=" N LEU F 369 " --> pdb=" O THR F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 374 No H-bonds generated for 'chain 'F' and resid 372 through 374' Processing helix chain 'F' and resid 376 through 381 removed outlier: 3.614A pdb=" N SER F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 385 removed outlier: 4.099A pdb=" N CYS F 385 " --> pdb=" O GLU F 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 382 through 385' Processing helix chain 'F' and resid 388 through 400 Processing helix chain 'F' and resid 430 through 435 removed outlier: 4.080A pdb=" N LYS F 435 " --> pdb=" O ASP F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 462 removed outlier: 3.707A pdb=" N GLU F 459 " --> pdb=" O SER F 455 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU F 460 " --> pdb=" O PRO F 456 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 469 Processing helix chain 'F' and resid 476 through 489 Processing helix chain 'F' and resid 508 through 521 Processing helix chain 'F' and resid 528 through 532 removed outlier: 4.038A pdb=" N ILE F 531 " --> pdb=" O GLY F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 548 removed outlier: 3.660A pdb=" N ILE F 544 " --> pdb=" O ASN F 541 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA F 545 " --> pdb=" O PRO F 542 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ASN F 546 " --> pdb=" O PHE F 543 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N HIS F 548 " --> pdb=" O ALA F 545 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 577 removed outlier: 3.738A pdb=" N LYS F 575 " --> pdb=" O SER F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 619 Processing helix chain 'F' and resid 632 through 634 No H-bonds generated for 'chain 'F' and resid 632 through 634' Processing helix chain 'F' and resid 635 through 641 removed outlier: 3.557A pdb=" N ALA F 639 " --> pdb=" O GLY F 635 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN F 641 " --> pdb=" O GLU F 637 " (cutoff:3.500A) Processing helix chain 'F' and resid 653 through 661 removed outlier: 4.127A pdb=" N GLY F 657 " --> pdb=" O GLU F 653 " (cutoff:3.500A) Processing helix chain 'F' and resid 664 through 680 Processing helix chain 'E' and resid 327 through 334 Processing helix chain 'E' and resid 367 through 372 Processing helix chain 'E' and resid 373 through 375 No H-bonds generated for 'chain 'E' and resid 373 through 375' Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 388 through 398 Processing helix chain 'E' and resid 429 through 435 removed outlier: 3.590A pdb=" N ASP E 432 " --> pdb=" O SER E 429 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS E 434 " --> pdb=" O ASP E 431 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS E 435 " --> pdb=" O ASP E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 467 removed outlier: 3.570A pdb=" N ASP E 467 " --> pdb=" O ASN E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 489 Processing helix chain 'E' and resid 508 through 521 Processing helix chain 'E' and resid 529 through 534 removed outlier: 3.522A pdb=" N THR E 533 " --> pdb=" O GLN E 529 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 546 removed outlier: 4.148A pdb=" N ALA E 545 " --> pdb=" O ASN E 541 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASN E 546 " --> pdb=" O PRO E 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 541 through 546' Processing helix chain 'E' and resid 570 through 577 Processing helix chain 'E' and resid 617 through 621 removed outlier: 4.188A pdb=" N ILE E 621 " --> pdb=" O MET E 618 " (cutoff:3.500A) Processing helix chain 'E' and resid 632 through 634 No H-bonds generated for 'chain 'E' and resid 632 through 634' Processing helix chain 'E' and resid 635 through 641 Processing helix chain 'E' and resid 653 through 661 removed outlier: 4.657A pdb=" N GLY E 657 " --> pdb=" O GLU E 653 " (cutoff:3.500A) Processing helix chain 'E' and resid 664 through 680 Processing sheet with id=AA1, first strand: chain 'C' and resid 339 through 341 Processing sheet with id=AA2, first strand: chain 'C' and resid 412 through 414 removed outlier: 3.525A pdb=" N MET C 426 " --> pdb=" O ASP C 421 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 524 through 526 removed outlier: 6.957A pdb=" N VAL C 525 " --> pdb=" O PHE C 554 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY C 503 " --> pdb=" O THR C 604 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N PHE C 500 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N PHE C 626 " --> pdb=" O PHE C 500 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N PHE C 502 " --> pdb=" O PHE C 626 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 581 through 582 Processing sheet with id=AA5, first strand: chain 'C' and resid 629 through 631 Processing sheet with id=AA6, first strand: chain 'B' and resid 349 through 350 Processing sheet with id=AA7, first strand: chain 'B' and resid 412 through 415 removed outlier: 3.967A pdb=" N GLY B 418 " --> pdb=" O PHE B 415 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 524 through 526 removed outlier: 6.881A pdb=" N VAL B 525 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR B 499 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N THR B 604 " --> pdb=" O THR B 499 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N PHE B 501 " --> pdb=" O THR B 604 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AB1, first strand: chain 'B' and resid 628 through 631 removed outlier: 6.365A pdb=" N HIS B 629 " --> pdb=" O LYS B 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 339 through 341 Processing sheet with id=AB3, first strand: chain 'D' and resid 412 through 415 removed outlier: 3.947A pdb=" N GLY D 418 " --> pdb=" O PHE D 415 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 524 through 527 removed outlier: 6.754A pdb=" N VAL D 525 " --> pdb=" O PHE D 554 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N SER D 556 " --> pdb=" O VAL D 525 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N THR D 527 " --> pdb=" O SER D 556 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N LEU D 558 " --> pdb=" O THR D 527 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY D 503 " --> pdb=" O THR D 604 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU D 498 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N VAL D 624 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE D 500 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N PHE D 626 " --> pdb=" O PHE D 500 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N PHE D 502 " --> pdb=" O PHE D 626 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 581 through 583 Processing sheet with id=AB6, first strand: chain 'A' and resid 339 through 341 Processing sheet with id=AB7, first strand: chain 'A' and resid 412 through 414 Processing sheet with id=AB8, first strand: chain 'A' and resid 524 through 526 removed outlier: 6.294A pdb=" N VAL A 553 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU A 498 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL A 624 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N PHE A 500 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N PHE A 626 " --> pdb=" O PHE A 500 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N PHE A 502 " --> pdb=" O PHE A 626 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 339 through 341 removed outlier: 3.545A pdb=" N ILE F 351 " --> pdb=" O SER F 354 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 412 through 415 Processing sheet with id=AC2, first strand: chain 'F' and resid 525 through 526 removed outlier: 6.394A pdb=" N VAL F 525 " --> pdb=" O PHE F 554 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL F 553 " --> pdb=" O ILE F 601 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ASP F 603 " --> pdb=" O VAL F 553 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE F 500 " --> pdb=" O VAL F 624 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 629 through 631 Processing sheet with id=AC4, first strand: chain 'E' and resid 339 through 341 Processing sheet with id=AC5, first strand: chain 'E' and resid 412 through 414 Processing sheet with id=AC6, first strand: chain 'E' and resid 525 through 526 removed outlier: 6.563A pdb=" N VAL E 525 " --> pdb=" O PHE E 554 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL E 553 " --> pdb=" O ILE E 601 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ASP E 603 " --> pdb=" O VAL E 553 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR E 604 " --> pdb=" O PHE E 501 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY E 503 " --> pdb=" O THR E 604 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N PHE E 500 " --> pdb=" O VAL E 624 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N PHE E 626 " --> pdb=" O PHE E 500 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N PHE E 502 " --> pdb=" O PHE E 626 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 581 through 582 Processing sheet with id=AC8, first strand: chain 'E' and resid 629 through 631 547 hydrogen bonds defined for protein. 1566 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: 2.48 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 5823 1.34 - 1.49: 4730 1.49 - 1.64: 7794 1.64 - 1.80: 47 1.80 - 1.95: 93 Bond restraints: 18487 Sorted by residual: bond pdb=" CA SER E 455 " pdb=" C SER E 455 " ideal model delta sigma weight residual 1.526 1.627 -0.102 1.47e-02 4.63e+03 4.77e+01 bond pdb=" N SER E 455 " pdb=" CA SER E 455 " ideal model delta sigma weight residual 1.456 1.499 -0.042 9.80e-03 1.04e+04 1.88e+01 bond pdb=" C ASP E 454 " pdb=" N SER E 455 " ideal model delta sigma weight residual 1.327 1.366 -0.040 1.05e-02 9.07e+03 1.44e+01 bond pdb=" CA CYS E 489 " pdb=" C CYS E 489 " ideal model delta sigma weight residual 1.523 1.565 -0.042 1.34e-02 5.57e+03 9.91e+00 bond pdb=" C3' DT S 2 " pdb=" C2' DT S 2 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.21e+00 ... (remaining 18482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 24407 1.88 - 3.77: 524 3.77 - 5.65: 73 5.65 - 7.54: 10 7.54 - 9.42: 6 Bond angle restraints: 25020 Sorted by residual: angle pdb=" N ILE F 364 " pdb=" CA ILE F 364 " pdb=" C ILE F 364 " ideal model delta sigma weight residual 110.42 105.30 5.12 9.60e-01 1.09e+00 2.85e+01 angle pdb=" N3 DT S 6 " pdb=" C4 DT S 6 " pdb=" O4 DT S 6 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.69e+01 angle pdb=" C GLY F 323 " pdb=" N ASN F 324 " pdb=" CA ASN F 324 " ideal model delta sigma weight residual 121.54 129.24 -7.70 1.91e+00 2.74e-01 1.63e+01 angle pdb=" N3 DT S 3 " pdb=" C4 DT S 3 " pdb=" O4 DT S 3 " ideal model delta sigma weight residual 119.90 122.31 -2.41 6.00e-01 2.78e+00 1.62e+01 angle pdb=" N3 DT S 4 " pdb=" C4 DT S 4 " pdb=" O4 DT S 4 " ideal model delta sigma weight residual 119.90 122.31 -2.41 6.00e-01 2.78e+00 1.61e+01 ... (remaining 25015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.18: 10657 33.18 - 66.35: 593 66.35 - 99.53: 36 99.53 - 132.71: 0 132.71 - 165.88: 4 Dihedral angle restraints: 11290 sinusoidal: 4811 harmonic: 6479 Sorted by residual: dihedral pdb=" C5' ADP E1001 " pdb=" O5' ADP E1001 " pdb=" PA ADP E1001 " pdb=" O2A ADP E1001 " ideal model delta sinusoidal sigma weight residual -60.00 -149.54 89.54 1 2.00e+01 2.50e-03 2.38e+01 dihedral pdb=" CA LYS E 366 " pdb=" C LYS E 366 " pdb=" N LEU E 367 " pdb=" CA LEU E 367 " ideal model delta harmonic sigma weight residual 180.00 156.18 23.82 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" O1A AGS C1001 " pdb=" O3A AGS C1001 " pdb=" PA AGS C1001 " pdb=" PB AGS C1001 " ideal model delta sinusoidal sigma weight residual 292.27 126.39 165.88 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 11287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2448 0.067 - 0.133: 340 0.133 - 0.200: 3 0.200 - 0.266: 1 0.266 - 0.333: 1 Chirality restraints: 2793 Sorted by residual: chirality pdb=" CA SER E 455 " pdb=" N SER E 455 " pdb=" C SER E 455 " pdb=" CB SER E 455 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA ILE F 364 " pdb=" N ILE F 364 " pdb=" C ILE F 364 " pdb=" CB ILE F 364 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA ILE A 683 " pdb=" N ILE A 683 " pdb=" C ILE A 683 " pdb=" CB ILE A 683 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.06e-01 ... (remaining 2790 not shown) Planarity restraints: 3162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 361 " -0.045 5.00e-02 4.00e+02 6.81e-02 7.41e+00 pdb=" N PRO D 362 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO D 362 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 362 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 361 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO B 362 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 362 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 362 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 484 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" C LYS D 484 " -0.033 2.00e-02 2.50e+03 pdb=" O LYS D 484 " 0.012 2.00e-02 2.50e+03 pdb=" N THR D 485 " 0.011 2.00e-02 2.50e+03 ... (remaining 3159 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 82 2.45 - 3.06: 10848 3.06 - 3.67: 25751 3.67 - 4.29: 40615 4.29 - 4.90: 68024 Nonbonded interactions: 145320 Sorted by model distance: nonbonded pdb=" OG SER C 510 " pdb="MG MG C1002 " model vdw 1.832 2.170 nonbonded pdb=" O3G AGS B1001 " pdb="MG MG B1002 " model vdw 1.990 2.170 nonbonded pdb=" OG SER A 510 " pdb="MG MG A1002 " model vdw 2.011 2.170 nonbonded pdb=" O3G AGS D1001 " pdb="MG MG D1002 " model vdw 2.013 2.170 nonbonded pdb=" O3G AGS A1001 " pdb="MG MG A1002 " model vdw 2.024 2.170 ... (remaining 145315 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 323 through 580 or resid 594 through 687 or resid 1002)) selection = (chain 'B' and (resid 323 through 580 or resid 594 through 687 or resid 1002)) selection = (chain 'C' and (resid 323 through 580 or resid 594 through 687 or resid 1002)) selection = (chain 'D' and (resid 323 through 580 or resid 594 through 687 or resid 1002)) selection = (chain 'E' and (resid 323 through 580 or resid 594 through 687 or resid 1002)) selection = (chain 'F' and (resid 323 through 687 or resid 1002)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 14.390 Find NCS groups from input model: 0.330 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:6.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 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 : 0.004 0.102 18487 Z= 0.198 Angle : 0.664 9.421 25020 Z= 0.377 Chirality : 0.044 0.333 2793 Planarity : 0.004 0.068 3162 Dihedral : 18.538 165.883 7086 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.01 % Favored : 93.94 % Rotamer: Outliers : 4.33 % Allowed : 25.86 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.18), residues: 2195 helix: -0.78 (0.18), residues: 776 sheet: -1.56 (0.26), residues: 412 loop : -1.38 (0.19), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 514 TYR 0.020 0.001 TYR D 482 PHE 0.018 0.001 PHE F 543 TRP 0.016 0.001 TRP F 675 HIS 0.004 0.001 HIS A 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.20 (18487) covalent geometry : angle 0.66358 / 0.38 (25020) hydrogen bonds : bond 0.19132 / 13.43 ( 547) hydrogen bonds : angle 6.67909 / 4.57 ( 1566) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 172 time to evaluate : 0.646 Fit side-chains REVERT: C 431 ASP cc_start: 0.8509 (t0) cc_final: 0.8287 (m-30) REVERT: F 547 MET cc_start: 0.6941 (mpt) cc_final: 0.6610 (mpt) outliers start: 87 outliers final: 74 residues processed: 251 average time/residue: 0.4906 time to fit residues: 138.6111 Evaluate side-chains 240 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 166 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 488 SER Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain D residue 695 ASP Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 346 ASP Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 372 ARG Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain F residue 429 SER Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 488 SER Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 614 ASP Chi-restraints excluded: chain F residue 648 VAL Chi-restraints excluded: chain F residue 674 LYS Chi-restraints excluded: chain E residue 331 GLN Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 487 SER Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 558 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 216 optimal weight: 0.0570 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 8.9990 overall best weight: 2.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 660 GLN B 529 GLN D 478 ASN A 324 ASN F 662 ASN E 478 ASN E 660 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.144164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.105330 restraints weight = 23043.731| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.02 r_work: 0.2922 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.0611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 18487 Z= 0.202 Angle : 0.646 9.543 25020 Z= 0.332 Chirality : 0.046 0.216 2793 Planarity : 0.005 0.059 3162 Dihedral : 12.959 168.224 2666 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.01 % Favored : 93.94 % Rotamer: Outliers : 5.42 % Allowed : 23.57 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.18), residues: 2195 helix: -0.37 (0.19), residues: 775 sheet: -1.53 (0.25), residues: 411 loop : -1.36 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 514 TYR 0.019 0.001 TYR C 482 PHE 0.013 0.002 PHE C 444 TRP 0.010 0.001 TRP F 675 HIS 0.005 0.001 HIS D 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.20 (18487) covalent geometry : angle 0.64608 / 0.33 (25020) hydrogen bonds : bond 0.05552 / 3.72 ( 547) hydrogen bonds : angle 4.95803 / 3.41 ( 1566) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 174 time to evaluate : 0.983 Fit side-chains REVERT: C 529 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8692 (pt0) REVERT: B 554 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.8576 (t80) REVERT: D 627 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8391 (mtp180) REVERT: A 617 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7076 (tp) REVERT: F 547 MET cc_start: 0.6995 (mpt) cc_final: 0.6717 (ptt) REVERT: F 664 TYR cc_start: 0.5380 (m-80) cc_final: 0.4839 (m-10) REVERT: E 457 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6435 (tt0) outliers start: 109 outliers final: 53 residues processed: 264 average time/residue: 0.6763 time to fit residues: 199.7819 Evaluate side-chains 214 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 156 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 571 SER Chi-restraints excluded: chain D residue 627 ARG Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 372 ARG Chi-restraints excluded: chain F residue 387 ARG Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain F residue 516 LEU Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 631 SER Chi-restraints excluded: chain F residue 648 VAL Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 457 GLU Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain E residue 631 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 30 optimal weight: 3.9990 chunk 209 optimal weight: 7.9990 chunk 152 optimal weight: 0.2980 chunk 150 optimal weight: 0.6980 chunk 156 optimal weight: 10.0000 chunk 142 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 214 optimal weight: 5.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 660 GLN B 529 GLN A 324 ASN A 478 ASN F 478 ASN F 662 ASN E 660 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.145759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.106789 restraints weight = 23032.645| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.99 r_work: 0.2951 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18487 Z= 0.131 Angle : 0.579 8.509 25020 Z= 0.298 Chirality : 0.043 0.229 2793 Planarity : 0.004 0.050 3162 Dihedral : 12.101 167.540 2603 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.28 % Favored : 94.67 % Rotamer: Outliers : 4.62 % Allowed : 24.56 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.18), residues: 2195 helix: -0.02 (0.19), residues: 769 sheet: -1.30 (0.27), residues: 383 loop : -1.28 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 514 TYR 0.017 0.001 TYR B 482 PHE 0.011 0.001 PHE F 444 TRP 0.008 0.001 TRP F 675 HIS 0.003 0.001 HIS D 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (18487) covalent geometry : angle 0.57895 / 0.30 (25020) hydrogen bonds : bond 0.04241 / 2.85 ( 547) hydrogen bonds : angle 4.56826 / 3.13 ( 1566) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 173 time to evaluate : 0.580 Fit side-chains REVERT: C 359 SER cc_start: 0.8669 (OUTLIER) cc_final: 0.8339 (t) REVERT: C 529 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8640 (pt0) REVERT: B 554 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.8609 (t80) REVERT: D 557 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6292 (mp0) REVERT: D 627 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8352 (mtp180) REVERT: A 581 CYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7649 (t) REVERT: F 413 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7093 (tm) REVERT: F 547 MET cc_start: 0.6838 (mpt) cc_final: 0.6520 (ptm) REVERT: F 618 MET cc_start: 0.6420 (OUTLIER) cc_final: 0.6148 (mmm) REVERT: E 478 ASN cc_start: 0.8157 (OUTLIER) cc_final: 0.7691 (t0) REVERT: E 636 ARG cc_start: 0.5072 (tmt90) cc_final: 0.4861 (tpt-90) outliers start: 93 outliers final: 55 residues processed: 253 average time/residue: 0.6225 time to fit residues: 176.0468 Evaluate side-chains 222 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 158 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 529 GLN Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain D residue 571 SER Chi-restraints excluded: chain D residue 627 ARG Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain D residue 695 ASP Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 581 CYS Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 372 ARG Chi-restraints excluded: chain F residue 387 ARG Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain F residue 516 LEU Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 618 MET Chi-restraints excluded: chain F residue 631 SER Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 478 ASN Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain E residue 631 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 90 optimal weight: 1.9990 chunk 180 optimal weight: 10.0000 chunk 69 optimal weight: 0.3980 chunk 30 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 159 optimal weight: 8.9990 chunk 198 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 181 optimal weight: 0.5980 chunk 157 optimal weight: 7.9990 chunk 170 optimal weight: 9.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 660 GLN B 529 GLN A 324 ASN A 478 ASN F 478 ASN F 662 ASN E 660 GLN E 680 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.146245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.107299 restraints weight = 22984.051| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.99 r_work: 0.2942 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18487 Z= 0.119 Angle : 0.564 8.713 25020 Z= 0.288 Chirality : 0.043 0.233 2793 Planarity : 0.004 0.044 3162 Dihedral : 11.814 167.910 2591 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.42 % Favored : 94.53 % Rotamer: Outliers : 4.92 % Allowed : 24.02 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.18), residues: 2195 helix: 0.20 (0.19), residues: 771 sheet: -1.22 (0.27), residues: 392 loop : -1.22 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 663 TYR 0.017 0.001 TYR B 482 PHE 0.010 0.001 PHE D 524 TRP 0.008 0.001 TRP F 675 HIS 0.003 0.001 HIS D 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (18487) covalent geometry : angle 0.56360 / 0.29 (25020) hydrogen bonds : bond 0.03882 / 2.60 ( 547) hydrogen bonds : angle 4.41223 / 3.02 ( 1566) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 177 time to evaluate : 0.668 Fit side-chains REVERT: C 529 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8640 (pt0) REVERT: B 554 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.8611 (t80) REVERT: D 557 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6306 (mp0) REVERT: D 607 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8117 (mtmm) REVERT: D 627 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8361 (mtp180) REVERT: A 581 CYS cc_start: 0.8515 (OUTLIER) cc_final: 0.7986 (t) REVERT: A 617 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7146 (tp) REVERT: A 640 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6838 (mt-10) REVERT: F 375 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8280 (mp) REVERT: F 413 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7295 (tm) REVERT: F 547 MET cc_start: 0.7003 (mpt) cc_final: 0.6468 (ptm) REVERT: F 649 LYS cc_start: 0.5587 (OUTLIER) cc_final: 0.5189 (mtpp) REVERT: E 457 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6577 (tp30) REVERT: E 618 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8108 (mmp) REVERT: E 636 ARG cc_start: 0.5147 (tmt90) cc_final: 0.4880 (tpt-90) outliers start: 99 outliers final: 51 residues processed: 257 average time/residue: 0.5902 time to fit residues: 170.1527 Evaluate side-chains 225 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 161 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 529 GLN Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain D residue 607 LYS Chi-restraints excluded: chain D residue 627 ARG Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain D residue 695 ASP Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 581 CYS Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 640 GLU Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 372 ARG Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 387 ARG Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 457 GLU Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain E residue 618 MET Chi-restraints excluded: chain E residue 631 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 127 optimal weight: 5.9990 chunk 63 optimal weight: 0.0980 chunk 124 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 189 optimal weight: 0.0870 chunk 192 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 660 GLN B 529 GLN A 324 ASN F 352 ASN F 662 ASN E 660 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.147612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.108839 restraints weight = 22824.418| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.99 r_work: 0.2973 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18487 Z= 0.099 Angle : 0.544 9.411 25020 Z= 0.278 Chirality : 0.042 0.240 2793 Planarity : 0.004 0.038 3162 Dihedral : 11.533 168.985 2585 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.24 % Favored : 94.72 % Rotamer: Outliers : 4.82 % Allowed : 24.12 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.18), residues: 2195 helix: 0.36 (0.19), residues: 781 sheet: -1.15 (0.29), residues: 362 loop : -1.18 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 663 TYR 0.015 0.001 TYR C 482 PHE 0.011 0.001 PHE F 543 TRP 0.009 0.001 TRP F 675 HIS 0.002 0.001 HIS A 629 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (18487) covalent geometry : angle 0.54422 / 0.28 (25020) hydrogen bonds : bond 0.03228 / 2.18 ( 547) hydrogen bonds : angle 4.22471 / 2.89 ( 1566) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 183 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: C 390 LYS cc_start: 0.8804 (mmpt) cc_final: 0.8592 (mttp) REVERT: C 529 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8621 (pt0) REVERT: B 471 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8948 (mt) REVERT: B 538 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7815 (mmpt) REVERT: B 554 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.8616 (t80) REVERT: D 557 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6293 (mp0) REVERT: D 607 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8123 (mtmm) REVERT: A 526 GLU cc_start: 0.8212 (tt0) cc_final: 0.7952 (tp30) REVERT: A 617 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7184 (tp) REVERT: A 637 GLU cc_start: 0.8529 (tp30) cc_final: 0.8236 (pm20) REVERT: F 375 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8253 (mp) REVERT: F 413 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7284 (tm) REVERT: F 547 MET cc_start: 0.6920 (mpt) cc_final: 0.6459 (ptm) REVERT: F 649 LYS cc_start: 0.5543 (OUTLIER) cc_final: 0.5222 (mtpp) REVERT: E 478 ASN cc_start: 0.8110 (OUTLIER) cc_final: 0.7657 (t0) REVERT: E 618 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8016 (mmp) REVERT: E 636 ARG cc_start: 0.5182 (tmt90) cc_final: 0.4931 (tpt-90) outliers start: 97 outliers final: 48 residues processed: 260 average time/residue: 0.5536 time to fit residues: 161.4301 Evaluate side-chains 229 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 169 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 529 GLN Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain D residue 607 LYS Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain D residue 695 ASP Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 387 ARG Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 478 ASN Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain E residue 618 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 156 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 167 optimal weight: 9.9990 chunk 138 optimal weight: 0.0970 chunk 25 optimal weight: 0.5980 chunk 123 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 73 optimal weight: 0.3980 chunk 90 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 660 GLN B 529 GLN A 324 ASN F 662 ASN E 660 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.147262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.108530 restraints weight = 22738.651| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.98 r_work: 0.2966 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18487 Z= 0.108 Angle : 0.556 9.510 25020 Z= 0.281 Chirality : 0.042 0.242 2793 Planarity : 0.004 0.035 3162 Dihedral : 11.411 169.031 2580 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.28 % Allowed : 24.66 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.18), residues: 2195 helix: 0.47 (0.19), residues: 779 sheet: -1.13 (0.29), residues: 362 loop : -1.17 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 514 TYR 0.016 0.001 TYR C 482 PHE 0.009 0.001 PHE D 588 TRP 0.009 0.001 TRP F 675 HIS 0.002 0.001 HIS D 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (18487) covalent geometry : angle 0.55619 / 0.28 (25020) hydrogen bonds : bond 0.03394 / 2.29 ( 547) hydrogen bonds : angle 4.16624 / 2.85 ( 1566) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 178 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: C 359 SER cc_start: 0.8559 (m) cc_final: 0.8281 (t) REVERT: C 393 GLU cc_start: 0.8475 (tt0) cc_final: 0.8253 (tm-30) REVERT: C 514 ARG cc_start: 0.8726 (mtt-85) cc_final: 0.8497 (mtm110) REVERT: C 529 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8647 (pt0) REVERT: B 538 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7818 (mmpt) REVERT: B 554 PHE cc_start: 0.9142 (OUTLIER) cc_final: 0.8621 (t80) REVERT: D 557 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6307 (mp0) REVERT: D 607 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8105 (mtmm) REVERT: D 612 ARG cc_start: 0.8264 (ttt180) cc_final: 0.7965 (ptt-90) REVERT: D 627 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8348 (mtp180) REVERT: A 526 GLU cc_start: 0.8189 (tt0) cc_final: 0.7951 (tp30) REVERT: A 617 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7193 (tp) REVERT: F 375 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8214 (mp) REVERT: F 413 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7294 (tm) REVERT: F 547 MET cc_start: 0.7023 (mpt) cc_final: 0.6596 (ptm) REVERT: F 618 MET cc_start: 0.6202 (OUTLIER) cc_final: 0.5942 (mmm) REVERT: F 649 LYS cc_start: 0.5524 (OUTLIER) cc_final: 0.5207 (mtpp) REVERT: E 478 ASN cc_start: 0.8072 (OUTLIER) cc_final: 0.7589 (t0) REVERT: E 636 ARG cc_start: 0.5187 (tmt90) cc_final: 0.4937 (tpt-90) outliers start: 86 outliers final: 52 residues processed: 248 average time/residue: 0.6026 time to fit residues: 167.4176 Evaluate side-chains 227 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 163 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 529 GLN Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain D residue 607 LYS Chi-restraints excluded: chain D residue 627 ARG Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain D residue 695 ASP Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 387 ARG Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 618 MET Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 478 ASN Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 571 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 105 optimal weight: 0.0570 chunk 42 optimal weight: 0.0970 chunk 90 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 197 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 478 ASN C 660 GLN B 529 GLN B 597 HIS A 324 ASN F 353 ASN F 662 ASN E 660 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.148436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.109799 restraints weight = 22993.436| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.00 r_work: 0.2986 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18487 Z= 0.095 Angle : 0.541 9.887 25020 Z= 0.273 Chirality : 0.042 0.246 2793 Planarity : 0.004 0.090 3162 Dihedral : 11.240 169.769 2577 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.83 % Allowed : 25.31 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.18), residues: 2195 helix: 0.67 (0.19), residues: 773 sheet: -1.10 (0.29), residues: 352 loop : -1.13 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 612 TYR 0.015 0.001 TYR C 482 PHE 0.009 0.001 PHE F 543 TRP 0.010 0.001 TRP F 675 HIS 0.002 0.000 HIS A 629 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (18487) covalent geometry : angle 0.54064 / 0.27 (25020) hydrogen bonds : bond 0.02986 / 2.02 ( 547) hydrogen bonds : angle 4.07214 / 2.78 ( 1566) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 177 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: C 359 SER cc_start: 0.8545 (m) cc_final: 0.8262 (t) REVERT: C 529 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8620 (pt0) REVERT: B 538 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7830 (mmpt) REVERT: B 554 PHE cc_start: 0.9138 (OUTLIER) cc_final: 0.8635 (t80) REVERT: D 557 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6309 (mp0) REVERT: D 607 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8092 (mtmm) REVERT: D 612 ARG cc_start: 0.8213 (ttt180) cc_final: 0.7962 (ptt-90) REVERT: D 627 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8352 (mtp180) REVERT: A 617 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7143 (tp) REVERT: A 637 GLU cc_start: 0.8452 (tp30) cc_final: 0.8168 (pm20) REVERT: A 684 MET cc_start: 0.6041 (tmm) cc_final: 0.5250 (ttm) REVERT: F 375 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8155 (mp) REVERT: F 413 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7312 (tm) REVERT: F 547 MET cc_start: 0.6885 (mpt) cc_final: 0.6368 (tmm) REVERT: F 618 MET cc_start: 0.6225 (OUTLIER) cc_final: 0.5963 (mmm) REVERT: F 649 LYS cc_start: 0.5512 (OUTLIER) cc_final: 0.5303 (mtpp) REVERT: E 478 ASN cc_start: 0.7987 (OUTLIER) cc_final: 0.7518 (t0) REVERT: E 636 ARG cc_start: 0.5213 (tmt90) cc_final: 0.4978 (tpt-90) outliers start: 77 outliers final: 42 residues processed: 238 average time/residue: 0.5963 time to fit residues: 159.1201 Evaluate side-chains 222 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 168 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 529 GLN Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain D residue 607 LYS Chi-restraints excluded: chain D residue 627 ARG Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 387 ARG Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 618 MET Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 478 ASN Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 571 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 109 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 199 optimal weight: 0.0670 chunk 39 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 176 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 660 GLN B 529 GLN A 324 ASN F 662 ASN E 660 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.146012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.107096 restraints weight = 22952.564| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.99 r_work: 0.2936 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18487 Z= 0.146 Angle : 0.594 9.745 25020 Z= 0.298 Chirality : 0.044 0.245 2793 Planarity : 0.004 0.068 3162 Dihedral : 11.323 168.062 2572 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 4.23 % Allowed : 25.11 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.18), residues: 2195 helix: 0.57 (0.19), residues: 774 sheet: -1.06 (0.29), residues: 362 loop : -1.10 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 612 TYR 0.018 0.001 TYR B 482 PHE 0.025 0.001 PHE F 543 TRP 0.012 0.001 TRP F 675 HIS 0.004 0.001 HIS D 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (18487) covalent geometry : angle 0.59432 / 0.30 (25020) hydrogen bonds : bond 0.03942 / 2.65 ( 547) hydrogen bonds : angle 4.22042 / 2.89 ( 1566) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 173 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: C 359 SER cc_start: 0.8612 (m) cc_final: 0.8291 (t) REVERT: C 390 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8516 (mttp) REVERT: C 529 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8675 (pt0) REVERT: B 538 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7809 (mmpt) REVERT: B 554 PHE cc_start: 0.9163 (OUTLIER) cc_final: 0.8585 (t80) REVERT: D 557 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6313 (mp0) REVERT: D 607 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8095 (mtmm) REVERT: D 627 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8381 (mtp180) REVERT: A 617 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7142 (tp) REVERT: A 637 GLU cc_start: 0.8464 (tp30) cc_final: 0.8136 (pm20) REVERT: F 375 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8174 (mp) REVERT: F 413 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7299 (tm) REVERT: F 543 PHE cc_start: 0.6645 (t80) cc_final: 0.6341 (t80) REVERT: F 547 MET cc_start: 0.6943 (mpt) cc_final: 0.6358 (tmm) REVERT: E 636 ARG cc_start: 0.5159 (tmt90) cc_final: 0.4918 (tpt-90) outliers start: 85 outliers final: 57 residues processed: 243 average time/residue: 0.5417 time to fit residues: 148.0107 Evaluate side-chains 229 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 162 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 390 LYS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 529 GLN Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain D residue 571 SER Chi-restraints excluded: chain D residue 607 LYS Chi-restraints excluded: chain D residue 627 ARG Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 387 ARG Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain E residue 631 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 163 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 99 optimal weight: 0.0010 chunk 50 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 478 ASN C 660 GLN B 529 GLN A 324 ASN F 662 ASN E 660 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.146993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.108198 restraints weight = 22911.689| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.06 r_work: 0.2948 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18487 Z= 0.113 Angle : 0.572 10.789 25020 Z= 0.288 Chirality : 0.042 0.243 2793 Planarity : 0.004 0.069 3162 Dihedral : 11.265 169.077 2572 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.93 % Allowed : 25.51 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.18), residues: 2195 helix: 0.63 (0.19), residues: 773 sheet: -1.09 (0.29), residues: 367 loop : -1.07 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 344 TYR 0.022 0.001 TYR F 606 PHE 0.015 0.001 PHE F 543 TRP 0.012 0.001 TRP F 675 HIS 0.003 0.001 HIS E 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (18487) covalent geometry : angle 0.57163 / 0.29 (25020) hydrogen bonds : bond 0.03440 / 2.32 ( 547) hydrogen bonds : angle 4.15467 / 2.84 ( 1566) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 172 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: C 359 SER cc_start: 0.8602 (OUTLIER) cc_final: 0.8295 (t) REVERT: C 529 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8647 (pt0) REVERT: B 538 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7816 (mmpt) REVERT: B 554 PHE cc_start: 0.9153 (OUTLIER) cc_final: 0.8612 (t80) REVERT: D 557 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6291 (mp0) REVERT: D 607 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8093 (mtmm) REVERT: D 612 ARG cc_start: 0.8077 (ttp-170) cc_final: 0.7788 (ptt-90) REVERT: D 627 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8340 (mtp180) REVERT: A 617 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7104 (tp) REVERT: A 637 GLU cc_start: 0.8419 (tp30) cc_final: 0.8071 (pm20) REVERT: F 375 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8153 (mp) REVERT: F 413 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7300 (tm) REVERT: F 547 MET cc_start: 0.6946 (mpt) cc_final: 0.6230 (tmm) REVERT: E 618 MET cc_start: 0.8584 (mmp) cc_final: 0.8151 (mmt) REVERT: E 636 ARG cc_start: 0.5213 (tmt90) cc_final: 0.4939 (tpt-90) outliers start: 79 outliers final: 52 residues processed: 237 average time/residue: 0.6336 time to fit residues: 168.1565 Evaluate side-chains 221 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 159 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 497 CYS Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 529 GLN Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain D residue 607 LYS Chi-restraints excluded: chain D residue 627 ARG Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 387 ARG Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 558 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 213 optimal weight: 9.9990 chunk 180 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 156 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 150 optimal weight: 0.4980 chunk 111 optimal weight: 0.2980 chunk 157 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 163 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 478 ASN C 660 GLN B 529 GLN A 324 ASN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 662 ASN E 660 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.147664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.109652 restraints weight = 22784.072| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.19 r_work: 0.2968 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18487 Z= 0.105 Angle : 0.565 11.216 25020 Z= 0.284 Chirality : 0.042 0.248 2793 Planarity : 0.004 0.087 3162 Dihedral : 11.183 169.579 2572 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.58 % Allowed : 25.96 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.65 (0.18), residues: 2195 helix: 0.74 (0.19), residues: 773 sheet: -0.99 (0.30), residues: 351 loop : -1.07 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 570 TYR 0.018 0.001 TYR F 606 PHE 0.010 0.001 PHE D 588 TRP 0.014 0.001 TRP F 675 HIS 0.002 0.001 HIS E 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 (18487) covalent geometry : angle 0.56494 / 0.28 (25020) hydrogen bonds : bond 0.03200 / 2.15 ( 547) hydrogen bonds : angle 4.08048 / 2.79 ( 1566) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 165 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: C 359 SER cc_start: 0.8579 (OUTLIER) cc_final: 0.8271 (t) REVERT: C 529 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8623 (pt0) REVERT: B 538 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7773 (mmpt) REVERT: B 554 PHE cc_start: 0.9150 (OUTLIER) cc_final: 0.8606 (t80) REVERT: D 557 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6268 (mp0) REVERT: D 607 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8086 (mtmm) REVERT: D 612 ARG cc_start: 0.8040 (ttp-170) cc_final: 0.7723 (ptt-90) REVERT: D 627 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8344 (mtp180) REVERT: A 458 MET cc_start: 0.8096 (tpt) cc_final: 0.7891 (tpp) REVERT: A 617 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.6995 (tp) REVERT: A 637 GLU cc_start: 0.8391 (tp30) cc_final: 0.8042 (pm20) REVERT: F 375 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8144 (mp) REVERT: F 404 VAL cc_start: 0.7784 (OUTLIER) cc_final: 0.7275 (m) REVERT: F 413 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7269 (tm) REVERT: F 543 PHE cc_start: 0.6777 (t80) cc_final: 0.6470 (t80) REVERT: F 547 MET cc_start: 0.6934 (mpt) cc_final: 0.6340 (tmm) REVERT: E 618 MET cc_start: 0.8557 (mmp) cc_final: 0.8113 (mmt) REVERT: E 636 ARG cc_start: 0.5226 (tmt90) cc_final: 0.4949 (tpt-90) outliers start: 72 outliers final: 51 residues processed: 225 average time/residue: 0.6379 time to fit residues: 161.5514 Evaluate side-chains 219 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 157 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 497 CYS Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 529 GLN Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain D residue 607 LYS Chi-restraints excluded: chain D residue 627 ARG Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 387 ARG Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 558 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 182 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 142 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 660 GLN B 529 GLN A 324 ASN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 662 ASN E 660 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.146230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.108112 restraints weight = 23043.073| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.97 r_work: 0.2956 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18487 Z= 0.143 Angle : 0.600 11.303 25020 Z= 0.302 Chirality : 0.044 0.250 2793 Planarity : 0.004 0.087 3162 Dihedral : 11.278 167.899 2572 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.58 % Allowed : 26.21 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.18), residues: 2195 helix: 0.66 (0.19), residues: 771 sheet: -1.03 (0.29), residues: 361 loop : -1.07 (0.19), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 570 TYR 0.018 0.001 TYR B 482 PHE 0.013 0.001 PHE F 444 TRP 0.015 0.001 TRP F 675 HIS 0.004 0.001 HIS D 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (18487) covalent geometry : angle 0.59957 / 0.30 (25020) hydrogen bonds : bond 0.03932 / 2.63 ( 547) hydrogen bonds : angle 4.20340 / 2.88 ( 1566) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5805.64 seconds wall clock time: 99 minutes 41.68 seconds (5981.68 seconds total)