Starting phenix.real_space_refine on Sat Jul 4 04:27:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hwg_35057/07_2026/8hwg_35057.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hwg_35057/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8hwg_35057/07_2026/8hwg_35057.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hwg_35057/07_2026/8hwg_35057.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hwg_35057/07_2026/8hwg_35057.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hwg_35057/07_2026/8hwg_35057.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hwg_35057/07_2026/8hwg_35057.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hwg_35057/07_2026/8hwg_35057.map" } 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-dev-6108/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: 3.85, per 1000 atoms: 0.21 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: 1.70 Conformation dependent library (CDL) restraints added in 739.1 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: 0.64 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: 2.89 Time building geometry restraints manager: 2.16 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: 525 3.77 - 5.65: 72 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: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.340 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.030 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:7.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.720 ------------------------------------------------------------------------------- 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= 0.197 Angle : 0.663 9.421 25020 Z= 0.376 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 0.66326 / 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 : 0.613 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: 0.5326 time to fit residues: 150.4449 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 : 0.589 ------------------------------------------------------------------------------- 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 = 0.144158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.105310 restraints weight = 23038.245| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.02 r_work: 0.2916 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.0633 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= 0.203 Angle : 0.646 9.531 25020 Z= 0.332 Chirality : 0.046 0.197 2793 Planarity : 0.005 0.059 3162 Dihedral : 12.944 168.341 2666 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.01 % Favored : 93.94 % Rotamer: Outliers : 5.22 % Allowed : 23.72 % 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: -1.64 (0.18), residues: 2195 helix: -0.38 (0.19), residues: 775 sheet: -1.52 (0.25), residues: 411 loop : -1.36 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 514 TYR 0.020 0.001 TYR C 482 PHE 0.013 0.002 PHE C 444 TRP 0.010 0.002 TRP F 675 HIS 0.005 0.001 HIS D 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.20 (18487) covalent geometry : angle 0.64558 / 0.33 (25020) hydrogen bonds : bond 0.05490 / 3.68 ( 547) hydrogen bonds : angle 4.95147 / 3.40 ( 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 278 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 173 time to evaluate : 0.573 Fit side-chains REVERT: C 529 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8685 (pt0) REVERT: B 554 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.8568 (t80) REVERT: D 627 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8388 (mtp180) REVERT: A 617 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7097 (tp) REVERT: F 547 MET cc_start: 0.6980 (mpt) cc_final: 0.6701 (ptt) REVERT: F 664 TYR cc_start: 0.5363 (m-80) cc_final: 0.4825 (m-80) REVERT: E 457 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.6446 (tt0) outliers start: 105 outliers final: 50 residues processed: 260 average time/residue: 0.5893 time to fit residues: 170.9377 Evaluate side-chains 209 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 154 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 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 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 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: 1.9990 chunk 150 optimal weight: 0.9980 chunk 156 optimal weight: 10.0000 chunk 142 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 75 optimal weight: 0.2980 chunk 159 optimal weight: 3.9990 chunk 214 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 331 GLN E 660 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.145912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.106958 restraints weight = 22999.756| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.99 r_work: 0.2956 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18487 Z= 0.123 Angle : 0.572 8.620 25020 Z= 0.294 Chirality : 0.043 0.202 2793 Planarity : 0.004 0.050 3162 Dihedral : 12.089 167.718 2602 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.10 % Favored : 94.85 % Rotamer: Outliers : 4.57 % Allowed : 24.42 % 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: -1.30 (0.18), residues: 2195 helix: 0.01 (0.19), residues: 769 sheet: -1.30 (0.27), residues: 393 loop : -1.27 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 514 TYR 0.017 0.001 TYR B 482 PHE 0.010 0.001 PHE F 444 TRP 0.007 0.001 TRP F 675 HIS 0.003 0.001 HIS D 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (18487) covalent geometry : angle 0.57229 / 0.29 (25020) hydrogen bonds : bond 0.04129 / 2.78 ( 547) hydrogen bonds : angle 4.55319 / 3.12 ( 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 270 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 178 time to evaluate : 0.756 Fit side-chains REVERT: C 529 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8636 (pt0) REVERT: B 554 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.8612 (t80) REVERT: D 557 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6302 (mp0) REVERT: D 627 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8376 (mtp180) REVERT: A 581 CYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7664 (t) REVERT: F 413 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7099 (tm) REVERT: F 547 MET cc_start: 0.6836 (mpt) cc_final: 0.6513 (ptm) REVERT: F 618 MET cc_start: 0.6442 (OUTLIER) cc_final: 0.6153 (mmm) REVERT: E 478 ASN cc_start: 0.8151 (OUTLIER) cc_final: 0.7679 (t0) REVERT: E 636 ARG cc_start: 0.5056 (tmt90) cc_final: 0.4841 (tpt-90) outliers start: 92 outliers final: 52 residues processed: 255 average time/residue: 0.6303 time to fit residues: 179.3185 Evaluate side-chains 219 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 159 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 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 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 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 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 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 401 VAL Chi-restraints excluded: chain A residue 426 MET 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 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 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 436 TYR 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 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: 8.9990 chunk 69 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 130 optimal weight: 0.1980 chunk 159 optimal weight: 10.0000 chunk 198 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 181 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 331 GLN E 660 GLN E 680 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.145842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.106858 restraints weight = 22987.210| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.99 r_work: 0.2955 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.0990 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= 0.130 Angle : 0.571 8.661 25020 Z= 0.293 Chirality : 0.043 0.205 2793 Planarity : 0.004 0.043 3162 Dihedral : 11.839 167.725 2589 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.65 % Favored : 94.31 % Rotamer: Outliers : 5.27 % Allowed : 23.62 % Favored : 71.11 % 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: -1.15 (0.18), residues: 2195 helix: 0.17 (0.19), residues: 771 sheet: -1.23 (0.27), residues: 392 loop : -1.22 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 663 TYR 0.017 0.001 TYR B 482 PHE 0.010 0.001 PHE F 444 TRP 0.009 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 0.57142 / 0.29 (25020) hydrogen bonds : bond 0.04045 / 2.71 ( 547) hydrogen bonds : angle 4.44184 / 3.04 ( 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 285 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 179 time to evaluate : 0.790 Fit side-chains REVERT: C 359 SER cc_start: 0.8617 (OUTLIER) cc_final: 0.8311 (t) REVERT: C 529 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8648 (pt0) REVERT: B 554 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.8602 (t80) REVERT: D 557 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6313 (mp0) REVERT: D 607 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8129 (mtmm) REVERT: D 627 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8386 (mtp180) REVERT: A 581 CYS cc_start: 0.8388 (OUTLIER) cc_final: 0.7792 (t) REVERT: A 617 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7154 (tp) REVERT: A 640 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6845 (mt-10) REVERT: F 375 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8297 (mp) REVERT: F 413 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7308 (tm) REVERT: F 547 MET cc_start: 0.6933 (mpt) cc_final: 0.6558 (ptm) REVERT: F 649 LYS cc_start: 0.5593 (OUTLIER) cc_final: 0.5190 (mtpp) REVERT: E 457 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6597 (tp30) REVERT: E 618 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8110 (mmp) REVERT: E 636 ARG cc_start: 0.5125 (tmt90) cc_final: 0.4880 (tpt-90) outliers start: 106 outliers final: 57 residues processed: 266 average time/residue: 0.6324 time to fit residues: 188.7250 Evaluate side-chains 237 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 166 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 346 ASP 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 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 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 634 SER 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 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 693 ILE Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 426 MET 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 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 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 452 VAL 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: 0.0670 chunk 124 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 189 optimal weight: 6.9990 chunk 192 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 660 GLN B 529 GLN A 324 ASN A 478 ASN F 662 ASN E 331 GLN E 660 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.144503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.105606 restraints weight = 22917.755| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.97 r_work: 0.2937 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18487 Z= 0.170 Angle : 0.606 9.083 25020 Z= 0.309 Chirality : 0.045 0.205 2793 Planarity : 0.004 0.040 3162 Dihedral : 11.825 166.826 2585 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.10 % Favored : 93.85 % Rotamer: Outliers : 5.77 % Allowed : 23.57 % 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: -1.17 (0.18), residues: 2195 helix: 0.12 (0.19), residues: 772 sheet: -1.25 (0.27), residues: 392 loop : -1.21 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 663 TYR 0.019 0.001 TYR C 482 PHE 0.013 0.001 PHE F 444 TRP 0.008 0.001 TRP F 675 HIS 0.005 0.001 HIS D 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (18487) covalent geometry : angle 0.60629 / 0.31 (25020) hydrogen bonds : bond 0.04544 / 3.05 ( 547) hydrogen bonds : angle 4.47903 / 3.08 ( 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 289 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 173 time to evaluate : 0.767 Fit side-chains REVERT: C 359 SER cc_start: 0.8653 (OUTLIER) cc_final: 0.8335 (t) REVERT: C 529 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8661 (pt0) REVERT: B 554 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.8596 (t80) REVERT: D 557 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6560 (mp0) REVERT: D 607 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8138 (mtmm) REVERT: D 627 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8383 (mtp180) REVERT: A 566 SER cc_start: 0.4809 (OUTLIER) cc_final: 0.4599 (t) REVERT: A 617 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7206 (tp) REVERT: A 637 GLU cc_start: 0.8429 (tp30) cc_final: 0.8144 (pm20) REVERT: A 640 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6761 (mt-10) REVERT: F 375 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8335 (mp) REVERT: F 413 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7309 (tm) REVERT: F 547 MET cc_start: 0.6960 (mpt) cc_final: 0.6515 (ptm) REVERT: F 649 LYS cc_start: 0.5437 (OUTLIER) cc_final: 0.5117 (mtpp) REVERT: F 664 TYR cc_start: 0.5093 (m-80) cc_final: 0.4669 (m-10) REVERT: E 457 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6658 (tp30) REVERT: E 478 ASN cc_start: 0.8241 (OUTLIER) cc_final: 0.7835 (t0) REVERT: E 636 ARG cc_start: 0.5139 (tmt90) cc_final: 0.4875 (tpt-90) outliers start: 116 outliers final: 65 residues processed: 270 average time/residue: 0.6339 time to fit residues: 191.9127 Evaluate side-chains 240 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 161 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 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 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 631 SER 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 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 D residue 695 ASP 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 426 MET 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 525 VAL Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 569 ILE 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 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 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 452 VAL Chi-restraints excluded: chain E residue 457 GLU 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 Chi-restraints excluded: chain E residue 631 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 156 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 167 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 25 optimal weight: 0.0870 chunk 123 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 189 optimal weight: 0.0370 chunk 73 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 83 optimal weight: 0.0170 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 660 GLN B 529 GLN A 324 ASN A 478 ASN F 352 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 = 0.3691 r_free = 0.3691 target = 0.147585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.108800 restraints weight = 22707.494| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.01 r_work: 0.2978 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1291 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= 0.096 Angle : 0.546 9.275 25020 Z= 0.278 Chirality : 0.041 0.215 2793 Planarity : 0.003 0.036 3162 Dihedral : 11.531 169.359 2584 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.88 % Allowed : 25.06 % 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: -0.93 (0.18), residues: 2195 helix: 0.41 (0.19), residues: 779 sheet: -1.10 (0.28), residues: 382 loop : -1.17 (0.19), residues: 1034 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 0.012 0.001 PHE F 543 TRP 0.007 0.001 TRP F 675 HIS 0.002 0.000 HIS A 629 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 (18487) covalent geometry : angle 0.54576 / 0.28 (25020) hydrogen bonds : bond 0.03174 / 2.12 ( 547) hydrogen bonds : angle 4.21022 / 2.88 ( 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 257 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 179 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: C 359 SER cc_start: 0.8599 (OUTLIER) cc_final: 0.8281 (t) REVERT: C 390 LYS cc_start: 0.8799 (mmpt) cc_final: 0.8595 (mttp) REVERT: C 529 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8624 (pt0) REVERT: B 554 PHE cc_start: 0.9140 (OUTLIER) cc_final: 0.8620 (t80) REVERT: D 377 LYS cc_start: 0.8289 (mmtt) cc_final: 0.7923 (tptp) REVERT: D 607 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8116 (mtmm) REVERT: D 627 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8346 (mtp180) REVERT: A 581 CYS cc_start: 0.8493 (OUTLIER) cc_final: 0.7871 (t) REVERT: F 375 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8249 (mp) REVERT: F 413 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7288 (tm) REVERT: F 543 PHE cc_start: 0.6771 (t80) cc_final: 0.6562 (t80) REVERT: F 547 MET cc_start: 0.7086 (mpt) cc_final: 0.6706 (ptm) REVERT: F 649 LYS cc_start: 0.5507 (OUTLIER) cc_final: 0.5194 (mtpp) REVERT: E 618 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8040 (mmp) REVERT: E 636 ARG cc_start: 0.5181 (tmt90) cc_final: 0.4924 (tpt-90) outliers start: 78 outliers final: 46 residues processed: 243 average time/residue: 0.6758 time to fit residues: 182.6771 Evaluate side-chains 227 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 171 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 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 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 624 VAL Chi-restraints excluded: chain B residue 631 SER 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 429 SER Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 529 GLN 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 D residue 695 ASP 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 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 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 649 LYS Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain E residue 436 TYR 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 618 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 105 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 162 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 660 GLN B 529 GLN A 324 ASN A 478 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 = 0.3662 r_free = 0.3662 target = 0.145150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.106165 restraints weight = 23006.876| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.00 r_work: 0.2917 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18487 Z= 0.152 Angle : 0.594 9.204 25020 Z= 0.300 Chirality : 0.044 0.212 2793 Planarity : 0.004 0.042 3162 Dihedral : 11.617 167.858 2584 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 4.72 % Allowed : 24.32 % Favored : 70.96 % 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: 0.33 (0.19), residues: 777 sheet: -1.16 (0.28), residues: 372 loop : -1.14 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 612 TYR 0.019 0.001 TYR B 482 PHE 0.012 0.001 PHE F 444 TRP 0.009 0.001 TRP F 675 HIS 0.004 0.001 HIS D 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 (18487) covalent geometry : angle 0.59353 / 0.30 (25020) hydrogen bonds : bond 0.04213 / 2.83 ( 547) hydrogen bonds : angle 4.32337 / 2.96 ( 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 267 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 172 time to evaluate : 0.785 Fit side-chains REVERT: C 359 SER cc_start: 0.8602 (OUTLIER) cc_final: 0.8288 (t) REVERT: C 390 LYS cc_start: 0.8828 (mmpt) cc_final: 0.8603 (mttp) REVERT: C 529 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8684 (pt0) REVERT: B 554 PHE cc_start: 0.9182 (OUTLIER) cc_final: 0.8580 (t80) REVERT: D 607 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8110 (mtmm) REVERT: D 612 ARG cc_start: 0.8253 (ttt180) cc_final: 0.7956 (ptt-90) REVERT: D 627 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8357 (mtp180) REVERT: D 693 ILE cc_start: 0.6921 (OUTLIER) cc_final: 0.6576 (mm) REVERT: A 581 CYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8172 (t) REVERT: A 617 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7165 (tp) REVERT: A 637 GLU cc_start: 0.8295 (tp30) cc_final: 0.8013 (pm20) REVERT: A 684 MET cc_start: 0.6092 (tmm) cc_final: 0.5227 (ttm) REVERT: F 375 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8231 (mp) REVERT: F 413 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7269 (tm) REVERT: F 547 MET cc_start: 0.6910 (mpt) cc_final: 0.6247 (tmm) REVERT: F 649 LYS cc_start: 0.5501 (OUTLIER) cc_final: 0.5198 (mtpp) REVERT: E 387 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.7255 (ptt-90) REVERT: E 636 ARG cc_start: 0.5108 (tmt90) cc_final: 0.4848 (tpt-90) outliers start: 95 outliers final: 63 residues processed: 250 average time/residue: 0.6195 time to fit residues: 174.2960 Evaluate side-chains 238 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 163 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 380 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 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 518 SER Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 571 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 631 SER 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 429 SER 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 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 D residue 695 ASP Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 449 THR 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 689 THR 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 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 F residue 649 LYS Chi-restraints excluded: chain E residue 387 ARG 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 480 GLU Chi-restraints excluded: chain E residue 488 SER 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 631 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 109 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 199 optimal weight: 0.0010 chunk 39 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 191 optimal weight: 6.9990 chunk 176 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 660 GLN B 529 GLN A 324 ASN A 478 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 = 0.147119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.108479 restraints weight = 22879.794| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.00 r_work: 0.2960 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18487 Z= 0.102 Angle : 0.554 9.648 25020 Z= 0.281 Chirality : 0.042 0.214 2793 Planarity : 0.004 0.091 3162 Dihedral : 11.435 169.519 2583 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.08 % Allowed : 25.11 % 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: -0.84 (0.18), residues: 2195 helix: 0.49 (0.19), residues: 779 sheet: -1.08 (0.29), residues: 362 loop : -1.11 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 663 TYR 0.018 0.001 TYR F 606 PHE 0.014 0.001 PHE F 543 TRP 0.008 0.001 TRP F 675 HIS 0.002 0.001 HIS E 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (18487) covalent geometry : angle 0.55438 / 0.28 (25020) hydrogen bonds : bond 0.03275 / 2.21 ( 547) hydrogen bonds : angle 4.15460 / 2.84 ( 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 262 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 180 time to evaluate : 0.659 Fit side-chains REVERT: C 359 SER cc_start: 0.8639 (OUTLIER) cc_final: 0.8283 (t) REVERT: C 529 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8642 (pt0) REVERT: B 554 PHE cc_start: 0.9149 (OUTLIER) cc_final: 0.8621 (t80) REVERT: D 603 ASP cc_start: 0.8440 (t0) cc_final: 0.8195 (t70) REVERT: D 607 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8085 (mtmm) REVERT: D 612 ARG cc_start: 0.8249 (ttt180) cc_final: 0.7972 (ptt-90) REVERT: D 627 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8347 (mtp180) REVERT: D 693 ILE cc_start: 0.6930 (OUTLIER) cc_final: 0.6589 (mm) REVERT: A 478 ASN cc_start: 0.8378 (OUTLIER) cc_final: 0.7656 (t0) REVERT: A 581 CYS cc_start: 0.8475 (OUTLIER) cc_final: 0.7775 (t) REVERT: A 617 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7223 (tp) REVERT: A 637 GLU cc_start: 0.8447 (tp30) cc_final: 0.8184 (pm20) REVERT: A 660 GLN cc_start: 0.8305 (tp40) cc_final: 0.8080 (tp40) REVERT: F 375 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8201 (mp) REVERT: F 413 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7279 (tm) REVERT: F 543 PHE cc_start: 0.6745 (t80) cc_final: 0.6529 (t80) REVERT: F 547 MET cc_start: 0.7060 (mpt) cc_final: 0.6477 (tmm) REVERT: F 618 MET cc_start: 0.6504 (OUTLIER) cc_final: 0.6277 (mmm) REVERT: F 649 LYS cc_start: 0.5467 (OUTLIER) cc_final: 0.5206 (mtpp) REVERT: E 636 ARG cc_start: 0.5170 (tmt90) cc_final: 0.4912 (tpt-90) outliers start: 82 outliers final: 49 residues processed: 244 average time/residue: 0.5931 time to fit residues: 161.9574 Evaluate side-chains 223 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 161 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 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 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 497 CYS Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 554 PHE 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 429 SER Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 529 GLN 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 D residue 695 ASP Chi-restraints excluded: chain A residue 374 GLN 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 525 VAL Chi-restraints excluded: chain A residue 581 CYS 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 618 MET Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 472 THR 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 543 PHE Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 558 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 163 optimal weight: 10.0000 chunk 114 optimal weight: 0.6980 chunk 99 optimal weight: 0.0980 chunk 50 optimal weight: 0.5980 chunk 144 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 181 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 660 GLN B 529 GLN A 324 ASN A 478 ASN F 353 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 = 0.3692 r_free = 0.3692 target = 0.147666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.108872 restraints weight = 22882.624| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.98 r_work: 0.2985 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 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 : 0.002 0.036 18487 Z= 0.100 Angle : 0.564 10.872 25020 Z= 0.286 Chirality : 0.042 0.217 2793 Planarity : 0.004 0.081 3162 Dihedral : 11.274 170.026 2576 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.63 % Allowed : 25.96 % Favored : 70.41 % 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: 0.62 (0.19), residues: 773 sheet: -1.02 (0.30), residues: 347 loop : -1.10 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 663 TYR 0.015 0.001 TYR C 482 PHE 0.010 0.001 PHE D 588 TRP 0.010 0.001 TRP F 675 HIS 0.002 0.001 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (18487) covalent geometry : angle 0.56360 / 0.29 (25020) hydrogen bonds : bond 0.03137 / 2.12 ( 547) hydrogen bonds : angle 4.12472 / 2.82 ( 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 247 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 174 time to evaluate : 0.737 Fit side-chains REVERT: C 359 SER cc_start: 0.8664 (OUTLIER) cc_final: 0.8321 (t) REVERT: C 529 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8618 (pt0) REVERT: C 643 ASP cc_start: 0.8082 (p0) cc_final: 0.7747 (t70) REVERT: B 554 PHE cc_start: 0.9144 (OUTLIER) cc_final: 0.8627 (t80) REVERT: D 603 ASP cc_start: 0.8415 (t0) cc_final: 0.8191 (t70) REVERT: D 607 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8081 (mtmm) REVERT: D 612 ARG cc_start: 0.8262 (ttt180) cc_final: 0.7962 (ptt-90) REVERT: D 693 ILE cc_start: 0.6933 (OUTLIER) cc_final: 0.6594 (mm) REVERT: A 581 CYS cc_start: 0.8499 (OUTLIER) cc_final: 0.7781 (t) REVERT: A 617 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7239 (tp) REVERT: A 637 GLU cc_start: 0.8460 (tp30) cc_final: 0.8164 (pm20) REVERT: A 660 GLN cc_start: 0.8307 (tp40) cc_final: 0.8085 (tp40) REVERT: A 684 MET cc_start: 0.5998 (tmm) cc_final: 0.5218 (ttm) REVERT: F 375 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8167 (mp) REVERT: F 413 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7289 (tm) REVERT: F 547 MET cc_start: 0.6985 (mpt) cc_final: 0.6340 (tmm) REVERT: F 618 MET cc_start: 0.6490 (OUTLIER) cc_final: 0.6248 (mmm) REVERT: F 649 LYS cc_start: 0.5468 (OUTLIER) cc_final: 0.5239 (mtpp) REVERT: E 618 MET cc_start: 0.8588 (mmp) cc_final: 0.8173 (mmt) REVERT: E 636 ARG cc_start: 0.5193 (tmt90) cc_final: 0.4931 (tpt-90) outliers start: 73 outliers final: 50 residues processed: 234 average time/residue: 0.6114 time to fit residues: 161.0979 Evaluate side-chains 226 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 165 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 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 380 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 497 CYS 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 359 SER Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 429 SER 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 607 LYS 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 374 GLN 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 581 CYS 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 408 THR Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 472 THR 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 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: 0.2980 chunk 100 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 156 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 163 optimal weight: 10.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 660 GLN B 529 GLN A 324 ASN A 478 ASN F 546 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 = 0.3682 r_free = 0.3682 target = 0.146752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.108151 restraints weight = 22818.575| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.03 r_work: 0.2956 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1524 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= 0.118 Angle : 0.584 11.249 25020 Z= 0.294 Chirality : 0.043 0.216 2793 Planarity : 0.004 0.096 3162 Dihedral : 11.289 169.260 2574 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % 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: -0.72 (0.18), residues: 2195 helix: 0.63 (0.19), residues: 771 sheet: -1.02 (0.30), residues: 347 loop : -1.06 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 570 TYR 0.017 0.001 TYR B 482 PHE 0.010 0.001 PHE D 588 TRP 0.013 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 0.58429 / 0.29 (25020) hydrogen bonds : bond 0.03550 / 2.39 ( 547) hydrogen bonds : angle 4.15745 / 2.85 ( 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 243 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 171 time to evaluate : 0.866 Fit side-chains REVERT: C 359 SER cc_start: 0.8653 (OUTLIER) cc_final: 0.8296 (t) REVERT: C 529 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8657 (pt0) REVERT: C 643 ASP cc_start: 0.8105 (p0) cc_final: 0.7758 (t70) REVERT: B 554 PHE cc_start: 0.9159 (OUTLIER) cc_final: 0.8620 (t80) REVERT: D 607 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8113 (mtmm) REVERT: D 612 ARG cc_start: 0.8267 (ttt180) cc_final: 0.7911 (ptt-90) REVERT: D 693 ILE cc_start: 0.6876 (OUTLIER) cc_final: 0.6520 (mm) REVERT: A 478 ASN cc_start: 0.8450 (OUTLIER) cc_final: 0.7673 (t0) REVERT: A 581 CYS cc_start: 0.8499 (OUTLIER) cc_final: 0.7768 (t) REVERT: A 617 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7172 (tp) REVERT: A 637 GLU cc_start: 0.8392 (tp30) cc_final: 0.8112 (pm20) REVERT: A 660 GLN cc_start: 0.8269 (tp40) cc_final: 0.8064 (tp40) REVERT: A 684 MET cc_start: 0.6000 (tmm) cc_final: 0.5212 (ttm) REVERT: F 375 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8200 (mp) REVERT: F 413 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7290 (tm) REVERT: F 543 PHE cc_start: 0.6792 (t80) cc_final: 0.6499 (t80) REVERT: F 547 MET cc_start: 0.6955 (mpt) cc_final: 0.6424 (tmm) REVERT: F 618 MET cc_start: 0.6310 (OUTLIER) cc_final: 0.6088 (mmm) REVERT: E 618 MET cc_start: 0.8588 (mmp) cc_final: 0.8147 (mmt) REVERT: E 636 ARG cc_start: 0.5258 (tmt90) cc_final: 0.4983 (tpt-90) outliers start: 72 outliers final: 52 residues processed: 230 average time/residue: 0.6104 time to fit residues: 158.6555 Evaluate side-chains 223 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 160 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 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 380 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 497 CYS 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 359 SER Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 429 SER 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 571 SER Chi-restraints excluded: chain D residue 607 LYS 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 374 GLN 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 525 VAL Chi-restraints excluded: chain A residue 581 CYS 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 F residue 618 MET 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 472 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 182 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 0.0670 chunk 142 optimal weight: 0.8980 chunk 146 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 660 GLN B 529 GLN D 642 ASN A 324 ASN A 478 ASN F 662 ASN E 331 GLN E 660 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.147454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.109012 restraints weight = 22999.885| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.04 r_work: 0.2982 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18487 Z= 0.106 Angle : 0.575 11.325 25020 Z= 0.290 Chirality : 0.042 0.218 2793 Planarity : 0.004 0.091 3162 Dihedral : 11.232 169.729 2574 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.43 % Allowed : 26.36 % 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: -0.68 (0.18), residues: 2195 helix: 0.68 (0.19), residues: 773 sheet: -1.01 (0.30), residues: 351 loop : -1.06 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 570 TYR 0.025 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 0.00238 / 0.11 (18487) covalent geometry : angle 0.57451 / 0.29 (25020) hydrogen bonds : bond 0.03258 / 2.19 ( 547) hydrogen bonds : angle 4.11069 / 2.81 ( 1566) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6052.74 seconds wall clock time: 104 minutes 5.52 seconds (6245.52 seconds total)