Starting phenix.real_space_refine on Mon Jun 16 07:12:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hwg_35057/06_2025/8hwg_35057.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hwg_35057/06_2025/8hwg_35057.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hwg_35057/06_2025/8hwg_35057.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hwg_35057/06_2025/8hwg_35057.map" model { file = "/net/cci-nas-00/data/ceres_data/8hwg_35057/06_2025/8hwg_35057.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hwg_35057/06_2025/8hwg_35057.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.38, per 1000 atoms: 0.63 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: 4.51 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 2.03 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: 5.59 Time building geometry restraints manager: 5.35 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=" C SER E 455 " pdb=" O SER E 455 " ideal model delta sigma weight residual 1.234 1.190 0.045 1.56e-02 4.11e+03 8.19e+00 ... (remaining 18482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 24421 1.88 - 3.77: 514 3.77 - 5.65: 69 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=" 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=" CA SER E 455 " pdb=" C SER E 455 " pdb=" N PRO E 456 " ideal model delta sigma weight residual 117.62 121.55 -3.93 1.03e+00 9.43e-01 1.46e+01 angle pdb=" O GLU F 361 " pdb=" C GLU F 361 " pdb=" N PRO F 362 " ideal model delta sigma weight residual 121.72 118.21 3.51 9.80e-01 1.04e+00 1.28e+01 angle pdb=" CA ASP A 603 " pdb=" CB ASP A 603 " pdb=" CG ASP A 603 " ideal model delta sigma weight residual 112.60 115.95 -3.35 1.00e+00 1.00e+00 1.12e+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: 2451 0.067 - 0.133: 337 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 42.000 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 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= 0.187 Angle : 0.659 9.421 25020 Z= 0.361 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (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 TRP 0.016 0.001 TRP F 675 HIS 0.004 0.001 HIS A 680 PHE 0.018 0.001 PHE F 543 TYR 0.020 0.001 TYR D 482 ARG 0.012 0.000 ARG F 514 Details of bonding type rmsd hydrogen bonds : bond 0.19132 ( 547) hydrogen bonds : angle 6.67909 ( 1566) covalent geometry : bond 0.00376 (18487) covalent geometry : angle 0.65888 (25020) *********************** 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 : 2.127 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: 1.3279 time to fit residues: 374.8965 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 : 2.210 ------------------------------------------------------------------------------- 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 183 optimal weight: 5.9990 chunk 164 optimal weight: 20.0000 chunk 91 optimal weight: 0.0570 chunk 56 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 170 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 197 optimal weight: 4.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 660 GLN B 529 GLN A 324 ASN F 478 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 = 0.3687 r_free = 0.3687 target = 0.146999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.108141 restraints weight = 22868.309| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.99 r_work: 0.2965 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.0685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18487 Z= 0.118 Angle : 0.572 7.950 25020 Z= 0.296 Chirality : 0.042 0.136 2793 Planarity : 0.004 0.054 3162 Dihedral : 12.672 169.424 2666 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.01 % Favored : 94.94 % Rotamer: Outliers : 3.98 % Allowed : 24.56 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.18), residues: 2195 helix: -0.10 (0.19), residues: 773 sheet: -1.40 (0.27), residues: 389 loop : -1.34 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 675 HIS 0.003 0.001 HIS A 629 PHE 0.011 0.001 PHE F 543 TYR 0.016 0.001 TYR C 482 ARG 0.005 0.000 ARG F 514 Details of bonding type rmsd hydrogen bonds : bond 0.04239 ( 547) hydrogen bonds : angle 4.75875 ( 1566) covalent geometry : bond 0.00262 (18487) covalent geometry : angle 0.57242 (25020) *********************** 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 268 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 188 time to evaluate : 2.286 Fit side-chains REVERT: C 529 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8627 (pt0) REVERT: B 554 PHE cc_start: 0.9150 (OUTLIER) cc_final: 0.8630 (t80) REVERT: D 591 LYS cc_start: 0.8836 (mmtm) cc_final: 0.8416 (mmmt) REVERT: A 361 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7177 (mm-30) REVERT: A 536 LEU cc_start: 0.6655 (OUTLIER) cc_final: 0.6451 (pp) REVERT: F 547 MET cc_start: 0.6971 (mpt) cc_final: 0.6722 (ptt) REVERT: F 664 TYR cc_start: 0.5310 (m-80) cc_final: 0.4769 (m-10) outliers start: 80 outliers final: 39 residues processed: 253 average time/residue: 1.3524 time to fit residues: 382.9636 Evaluate side-chains 203 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 160 time to evaluate : 2.280 ------------------------------------------------------------------------------- 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 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 449 THR Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 536 LEU 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 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 525 VAL Chi-restraints excluded: chain F residue 631 SER Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 497 CYS 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 106 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 208 optimal weight: 10.0000 chunk 123 optimal weight: 0.0970 chunk 170 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 660 GLN B 529 GLN D 478 ASN A 324 ASN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3637 r_free = 0.3637 target = 0.142868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.103903 restraints weight = 22897.790| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.98 r_work: 0.2901 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 18487 Z= 0.253 Angle : 0.682 9.654 25020 Z= 0.348 Chirality : 0.048 0.166 2793 Planarity : 0.005 0.052 3162 Dihedral : 12.167 167.389 2586 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.42 % Favored : 93.53 % Rotamer: Outliers : 5.27 % Allowed : 23.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.18), residues: 2195 helix: -0.24 (0.19), residues: 773 sheet: -1.27 (0.26), residues: 412 loop : -1.28 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 355 HIS 0.007 0.002 HIS D 548 PHE 0.015 0.002 PHE F 444 TYR 0.023 0.002 TYR C 482 ARG 0.007 0.001 ARG F 570 Details of bonding type rmsd hydrogen bonds : bond 0.05990 ( 547) hydrogen bonds : angle 4.82822 ( 1566) covalent geometry : bond 0.00622 (18487) covalent geometry : angle 0.68205 (25020) *********************** 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 271 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 165 time to evaluate : 2.240 Fit side-chains REVERT: C 529 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8682 (pt0) REVERT: D 557 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6121 (mp0) REVERT: D 627 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8310 (mtp180) REVERT: A 581 CYS cc_start: 0.8477 (OUTLIER) cc_final: 0.7931 (t) REVERT: A 617 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7151 (tp) REVERT: F 547 MET cc_start: 0.6881 (mpt) cc_final: 0.6527 (ptm) REVERT: E 372 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8262 (ttp-170) REVERT: E 478 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.7772 (t0) REVERT: E 636 ARG cc_start: 0.5128 (tmt90) cc_final: 0.4849 (tpt-90) outliers start: 106 outliers final: 56 residues processed: 251 average time/residue: 1.4148 time to fit residues: 395.2377 Evaluate side-chains 220 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 157 time to evaluate : 2.310 ------------------------------------------------------------------------------- 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 346 ASP Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 497 CYS 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 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 572 ASP Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 359 SER 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 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 634 SER Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain D residue 695 ASP Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 426 MET 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 F residue 334 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 ILE 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 599 THR Chi-restraints excluded: chain F residue 631 SER Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 478 ASN Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 100 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 177 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 215 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 660 GLN B 529 GLN A 324 ASN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 662 ASN E 660 GLN E 680 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.146312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.107563 restraints weight = 22858.381| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.93 r_work: 0.2963 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18487 Z= 0.114 Angle : 0.560 8.786 25020 Z= 0.288 Chirality : 0.042 0.142 2793 Planarity : 0.004 0.045 3162 Dihedral : 11.748 168.083 2585 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.06 % Favored : 94.90 % Rotamer: Outliers : 4.62 % Allowed : 24.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.18), residues: 2195 helix: 0.17 (0.19), residues: 766 sheet: -1.25 (0.27), residues: 393 loop : -1.22 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 675 HIS 0.003 0.001 HIS D 548 PHE 0.015 0.001 PHE F 543 TYR 0.015 0.001 TYR C 482 ARG 0.007 0.000 ARG B 612 Details of bonding type rmsd hydrogen bonds : bond 0.03751 ( 547) hydrogen bonds : angle 4.42695 ( 1566) covalent geometry : bond 0.00260 (18487) covalent geometry : angle 0.56007 (25020) *********************** 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 270 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 177 time to evaluate : 3.397 Fit side-chains REVERT: C 529 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8636 (pt0) REVERT: B 554 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.8615 (t80) REVERT: D 557 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6278 (mp0) REVERT: D 607 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8134 (mtmm) REVERT: D 627 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8337 (mtp180) REVERT: A 581 CYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7582 (t) REVERT: A 617 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7203 (tp) REVERT: A 640 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.6848 (mt-10) REVERT: F 413 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7103 (tm) REVERT: F 547 MET cc_start: 0.7031 (mpt) cc_final: 0.6565 (ptm) REVERT: F 649 LYS cc_start: 0.5588 (OUTLIER) cc_final: 0.5179 (mtpp) REVERT: E 457 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6612 (tp30) REVERT: E 478 ASN cc_start: 0.8123 (OUTLIER) cc_final: 0.7654 (t0) REVERT: E 618 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8116 (mmp) REVERT: E 636 ARG cc_start: 0.5117 (tmt90) cc_final: 0.4825 (tpt-90) outliers start: 93 outliers final: 43 residues processed: 254 average time/residue: 1.8562 time to fit residues: 525.3837 Evaluate side-chains 215 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 159 time to evaluate : 2.376 ------------------------------------------------------------------------------- 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 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 529 GLN Chi-restraints excluded: chain C residue 544 ILE 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 681 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 529 GLN Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain D residue 607 LYS Chi-restraints excluded: chain D residue 627 ARG Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 436 TYR 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 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 649 LYS Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 457 GLU 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 618 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 125 optimal weight: 4.9990 chunk 15 optimal weight: 0.0570 chunk 148 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 171 optimal weight: 7.9990 chunk 201 optimal weight: 6.9990 chunk 94 optimal weight: 0.2980 chunk 178 optimal weight: 5.9990 overall best weight: 1.0704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3672 r_free = 0.3672 target = 0.145928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.107115 restraints weight = 23047.167| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.04 r_work: 0.2930 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18487 Z= 0.125 Angle : 0.570 9.207 25020 Z= 0.291 Chirality : 0.042 0.143 2793 Planarity : 0.004 0.041 3162 Dihedral : 11.623 168.082 2583 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.74 % Favored : 94.21 % Rotamer: Outliers : 4.62 % Allowed : 24.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.18), residues: 2195 helix: 0.27 (0.19), residues: 775 sheet: -1.17 (0.27), residues: 392 loop : -1.15 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 675 HIS 0.003 0.001 HIS D 548 PHE 0.011 0.001 PHE F 444 TYR 0.017 0.001 TYR B 482 ARG 0.005 0.000 ARG E 663 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 547) hydrogen bonds : angle 4.34080 ( 1566) covalent geometry : bond 0.00295 (18487) covalent geometry : angle 0.57043 (25020) *********************** 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 262 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 169 time to evaluate : 2.064 Fit side-chains REVERT: C 359 SER cc_start: 0.8590 (OUTLIER) cc_final: 0.8292 (t) REVERT: C 390 LYS cc_start: 0.8824 (mmpt) cc_final: 0.8611 (mttp) REVERT: C 529 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8651 (pt0) REVERT: B 554 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.8602 (t80) REVERT: D 557 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6192 (mp0) REVERT: D 607 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8119 (mtmm) REVERT: D 627 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8343 (mtp180) REVERT: A 526 GLU cc_start: 0.8225 (tt0) cc_final: 0.8018 (mt-10) REVERT: A 581 CYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7673 (t) REVERT: A 617 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7143 (tp) REVERT: F 375 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8291 (mp) REVERT: F 413 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7246 (tm) REVERT: F 547 MET cc_start: 0.6994 (mpt) cc_final: 0.6582 (ptm) REVERT: F 649 LYS cc_start: 0.5562 (OUTLIER) cc_final: 0.5166 (mtpp) REVERT: E 457 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6640 (tp30) REVERT: E 478 ASN cc_start: 0.8066 (OUTLIER) cc_final: 0.7596 (t0) REVERT: E 618 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8069 (mmp) REVERT: E 636 ARG cc_start: 0.5123 (tmt90) cc_final: 0.4859 (tpt-90) outliers start: 93 outliers final: 53 residues processed: 248 average time/residue: 1.3292 time to fit residues: 369.1336 Evaluate side-chains 224 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 157 time to evaluate : 2.562 ------------------------------------------------------------------------------- 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 346 ASP 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 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 581 CYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 406 THR 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 529 GLN Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain D residue 607 LYS Chi-restraints excluded: chain D residue 627 ARG Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 478 ASN 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 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 578 THR Chi-restraints excluded: chain F residue 649 LYS 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 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 618 MET 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 174 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 202 optimal weight: 8.9990 chunk 143 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 198 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3668 r_free = 0.3668 target = 0.145608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.106834 restraints weight = 23069.781| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.04 r_work: 0.2931 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18487 Z= 0.140 Angle : 0.579 9.374 25020 Z= 0.294 Chirality : 0.043 0.142 2793 Planarity : 0.004 0.039 3162 Dihedral : 11.603 167.854 2583 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.87 % Allowed : 24.27 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.18), residues: 2195 helix: 0.35 (0.19), residues: 768 sheet: -1.17 (0.27), residues: 392 loop : -1.16 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 675 HIS 0.003 0.001 HIS D 548 PHE 0.011 0.001 PHE F 444 TYR 0.018 0.001 TYR B 482 ARG 0.005 0.000 ARG E 663 Details of bonding type rmsd hydrogen bonds : bond 0.04023 ( 547) hydrogen bonds : angle 4.33312 ( 1566) covalent geometry : bond 0.00336 (18487) covalent geometry : angle 0.57857 (25020) *********************** 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 265 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 167 time to evaluate : 2.126 Fit side-chains REVERT: C 529 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8659 (pt0) REVERT: B 538 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7862 (mmpt) REVERT: B 554 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.8618 (t80) REVERT: B 618 MET cc_start: 0.8915 (mmp) cc_final: 0.8631 (mmp) REVERT: D 557 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6178 (mp0) REVERT: D 607 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8139 (mtmm) REVERT: D 627 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8368 (mtp180) REVERT: A 581 CYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7615 (t) REVERT: A 617 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7233 (tp) REVERT: F 375 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8266 (mp) REVERT: F 413 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7243 (tm) REVERT: F 547 MET cc_start: 0.7083 (mpt) cc_final: 0.6660 (ptm) REVERT: F 649 LYS cc_start: 0.5646 (OUTLIER) cc_final: 0.5233 (mtpp) REVERT: E 387 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7281 (ptt-90) REVERT: E 457 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6783 (tt0) REVERT: E 478 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7653 (t0) REVERT: E 618 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.7990 (mmp) REVERT: E 636 ARG cc_start: 0.5136 (tmt90) cc_final: 0.4869 (tpt-90) outliers start: 98 outliers final: 60 residues processed: 247 average time/residue: 1.3379 time to fit residues: 370.4975 Evaluate side-chains 234 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 159 time to evaluate : 2.115 ------------------------------------------------------------------------------- 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 346 ASP 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 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 538 LYS Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 406 THR 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 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 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 478 ASN 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 589 SER Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 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 578 THR Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 387 ARG 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 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 618 MET Chi-restraints excluded: chain E residue 631 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 83 optimal weight: 0.5980 chunk 207 optimal weight: 1.9990 chunk 184 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 213 optimal weight: 9.9990 chunk 154 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 148 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 86 optimal weight: 0.0370 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 660 GLN B 324 ASN B 529 GLN B 597 HIS A 324 ASN A 478 ASN F 352 ASN F 662 ASN E 660 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.147282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.108632 restraints weight = 22830.667| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.00 r_work: 0.2977 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 18487 Z= 0.103 Angle : 0.547 9.328 25020 Z= 0.279 Chirality : 0.041 0.136 2793 Planarity : 0.004 0.080 3162 Dihedral : 11.422 169.246 2583 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.93 % Allowed : 25.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.18), residues: 2195 helix: 0.49 (0.19), residues: 773 sheet: -1.08 (0.28), residues: 382 loop : -1.11 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 675 HIS 0.002 0.001 HIS D 347 PHE 0.010 0.001 PHE C 524 TYR 0.015 0.001 TYR C 482 ARG 0.007 0.000 ARG E 663 Details of bonding type rmsd hydrogen bonds : bond 0.03258 ( 547) hydrogen bonds : angle 4.19910 ( 1566) covalent geometry : bond 0.00232 (18487) covalent geometry : angle 0.54723 (25020) *********************** 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 251 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 172 time to evaluate : 2.167 Fit side-chains revert: symmetry clash REVERT: C 529 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8640 (pt0) REVERT: B 538 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7838 (mmpt) REVERT: B 554 PHE cc_start: 0.9183 (OUTLIER) cc_final: 0.8627 (t80) REVERT: B 618 MET cc_start: 0.8895 (mmp) cc_final: 0.8595 (mmp) REVERT: D 557 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6325 (mp0) REVERT: D 607 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8117 (mtmm) REVERT: D 627 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8363 (mtp180) REVERT: A 478 ASN cc_start: 0.8342 (OUTLIER) cc_final: 0.7415 (t0) REVERT: A 581 CYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7654 (t) REVERT: A 617 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7198 (tp) REVERT: A 640 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: F 375 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8231 (mp) REVERT: F 413 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7269 (tm) REVERT: F 543 PHE cc_start: 0.6803 (t80) cc_final: 0.6573 (t80) REVERT: F 547 MET cc_start: 0.6990 (mpt) cc_final: 0.6474 (tmm) REVERT: F 649 LYS cc_start: 0.5477 (OUTLIER) cc_final: 0.5207 (mtpp) REVERT: E 478 ASN cc_start: 0.8057 (OUTLIER) cc_final: 0.7594 (t0) REVERT: E 636 ARG cc_start: 0.5200 (tmt90) cc_final: 0.4972 (tpt-90) outliers start: 79 outliers final: 48 residues processed: 238 average time/residue: 1.3755 time to fit residues: 366.8913 Evaluate side-chains 225 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 163 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ARG 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 529 GLN Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 631 SER 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 497 CYS Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 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 557 GLU Chi-restraints excluded: chain D residue 607 LYS Chi-restraints excluded: chain D residue 627 ARG Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 478 ASN 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 640 GLU 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 649 LYS Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 478 ASN Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 558 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 191 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3680 r_free = 0.3680 target = 0.146628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.107848 restraints weight = 22886.494| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.99 r_work: 0.2951 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18487 Z= 0.126 Angle : 0.568 9.694 25020 Z= 0.289 Chirality : 0.042 0.138 2793 Planarity : 0.004 0.071 3162 Dihedral : 11.399 168.743 2581 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.18 % Allowed : 24.91 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.18), residues: 2195 helix: 0.52 (0.19), residues: 771 sheet: -1.11 (0.29), residues: 362 loop : -1.13 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 675 HIS 0.003 0.001 HIS D 548 PHE 0.010 0.001 PHE F 444 TYR 0.017 0.001 TYR B 482 ARG 0.007 0.000 ARG A 479 Details of bonding type rmsd hydrogen bonds : bond 0.03636 ( 547) hydrogen bonds : angle 4.21499 ( 1566) covalent geometry : bond 0.00299 (18487) covalent geometry : angle 0.56773 (25020) *********************** 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 247 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 163 time to evaluate : 2.714 Fit side-chains REVERT: C 359 SER cc_start: 0.8610 (OUTLIER) cc_final: 0.8297 (t) REVERT: C 529 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8654 (pt0) REVERT: B 538 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7836 (mmpt) REVERT: B 554 PHE cc_start: 0.9191 (OUTLIER) cc_final: 0.8624 (t80) REVERT: B 618 MET cc_start: 0.8878 (mmp) cc_final: 0.8555 (mmp) REVERT: D 557 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6281 (mp0) REVERT: D 607 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8109 (mtmm) REVERT: D 612 ARG cc_start: 0.8308 (ttt180) cc_final: 0.7967 (ptt-90) REVERT: D 627 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8364 (mtp180) REVERT: D 693 ILE cc_start: 0.6866 (OUTLIER) cc_final: 0.6520 (mm) REVERT: A 581 CYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7671 (t) REVERT: A 617 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7235 (tp) REVERT: A 684 MET cc_start: 0.5903 (tmm) cc_final: 0.5233 (ttm) REVERT: F 375 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8233 (mp) REVERT: F 413 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7255 (tm) REVERT: F 547 MET cc_start: 0.7074 (mpt) cc_final: 0.6440 (tmm) REVERT: F 649 LYS cc_start: 0.5435 (OUTLIER) cc_final: 0.5209 (mtpp) REVERT: E 478 ASN cc_start: 0.8043 (OUTLIER) cc_final: 0.7572 (t0) REVERT: E 636 ARG cc_start: 0.5224 (tmt90) cc_final: 0.4984 (tpt-90) outliers start: 84 outliers final: 51 residues processed: 234 average time/residue: 1.4185 time to fit residues: 371.8811 Evaluate side-chains 224 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 159 time to evaluate : 2.038 ------------------------------------------------------------------------------- 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 346 ASP 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 631 SER Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain C residue 649 LYS 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 538 LYS Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain D residue 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 557 GLU Chi-restraints excluded: chain D residue 607 LYS Chi-restraints excluded: chain D residue 627 ARG Chi-restraints excluded: chain D residue 634 SER Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain D residue 695 ASP Chi-restraints excluded: chain A residue 401 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 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 649 LYS Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 478 ASN Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain E residue 631 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 92 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 59 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 205 optimal weight: 0.0060 chunk 135 optimal weight: 0.1980 chunk 204 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3702 r_free = 0.3702 target = 0.148484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.109918 restraints weight = 23015.372| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.97 r_work: 0.3004 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 18487 Z= 0.095 Angle : 0.544 10.584 25020 Z= 0.275 Chirality : 0.041 0.133 2793 Planarity : 0.004 0.065 3162 Dihedral : 11.217 170.618 2579 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.18 % Allowed : 26.31 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.18), residues: 2195 helix: 0.68 (0.19), residues: 773 sheet: -1.07 (0.29), residues: 350 loop : -1.09 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 675 HIS 0.002 0.000 HIS D 347 PHE 0.014 0.001 PHE F 543 TYR 0.015 0.001 TYR C 482 ARG 0.007 0.000 ARG E 663 Details of bonding type rmsd hydrogen bonds : bond 0.02885 ( 547) hydrogen bonds : angle 4.07495 ( 1566) covalent geometry : bond 0.00213 (18487) covalent geometry : angle 0.54369 (25020) *********************** 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 243 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 179 time to evaluate : 2.335 Fit side-chains revert: symmetry clash REVERT: C 359 SER cc_start: 0.8642 (OUTLIER) cc_final: 0.8295 (t) REVERT: C 529 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8615 (pt0) REVERT: B 554 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.8629 (t80) REVERT: B 618 MET cc_start: 0.8888 (mmp) cc_final: 0.8622 (mmp) REVERT: D 360 GLU cc_start: 0.8417 (pm20) cc_final: 0.8212 (pm20) REVERT: D 557 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6277 (mp0) REVERT: D 627 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8343 (mtp180) REVERT: A 581 CYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7432 (t) REVERT: A 617 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7179 (tp) REVERT: A 684 MET cc_start: 0.5804 (tmm) cc_final: 0.5188 (ttm) REVERT: F 375 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8177 (mp) REVERT: F 413 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7298 (tm) REVERT: F 518 SER cc_start: 0.7529 (OUTLIER) cc_final: 0.7062 (p) REVERT: F 547 MET cc_start: 0.6881 (mpt) cc_final: 0.6450 (tmm) REVERT: F 618 MET cc_start: 0.6366 (mmt) cc_final: 0.6144 (mmm) REVERT: E 478 ASN cc_start: 0.8037 (OUTLIER) cc_final: 0.7577 (t0) REVERT: E 618 MET cc_start: 0.8573 (mmp) cc_final: 0.8149 (mmt) REVERT: E 636 ARG cc_start: 0.5358 (tmt90) cc_final: 0.5061 (tpt-90) outliers start: 64 outliers final: 35 residues processed: 231 average time/residue: 1.6745 time to fit residues: 435.4273 Evaluate side-chains 214 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 168 time to evaluate : 2.791 ------------------------------------------------------------------------------- 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 631 SER Chi-restraints excluded: chain C residue 649 LYS 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 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 627 ARG Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 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 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 518 SER Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 478 ASN Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 558 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 170 optimal weight: 5.9990 chunk 188 optimal weight: 0.5980 chunk 182 optimal weight: 1.9990 chunk 152 optimal weight: 0.4980 chunk 143 optimal weight: 2.9990 chunk 58 optimal weight: 0.0030 chunk 154 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 162 optimal weight: 10.0000 chunk 180 optimal weight: 6.9990 overall best weight: 1.2194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3679 r_free = 0.3679 target = 0.146642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.108337 restraints weight = 22857.154| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.96 r_work: 0.2959 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18487 Z= 0.133 Angle : 0.582 11.238 25020 Z= 0.294 Chirality : 0.043 0.140 2793 Planarity : 0.004 0.064 3162 Dihedral : 11.229 168.987 2571 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.23 % Allowed : 26.60 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.18), residues: 2195 helix: 0.62 (0.19), residues: 772 sheet: -1.06 (0.29), residues: 361 loop : -1.07 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 675 HIS 0.003 0.001 HIS E 548 PHE 0.011 0.001 PHE B 524 TYR 0.018 0.001 TYR B 482 ARG 0.010 0.000 ARG C 514 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 547) hydrogen bonds : angle 4.17041 ( 1566) covalent geometry : bond 0.00319 (18487) covalent geometry : angle 0.58186 (25020) ********************** 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 234 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 169 time to evaluate : 2.751 Fit side-chains REVERT: C 359 SER cc_start: 0.8667 (OUTLIER) cc_final: 0.8312 (t) REVERT: C 529 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8666 (pt0) REVERT: B 554 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.8602 (t80) REVERT: D 360 GLU cc_start: 0.8460 (pm20) cc_final: 0.8260 (pm20) REVERT: D 557 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6125 (mp0) REVERT: D 607 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8103 (mtmm) REVERT: D 627 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8384 (mtp180) REVERT: D 693 ILE cc_start: 0.6846 (OUTLIER) cc_final: 0.6493 (mm) REVERT: A 478 ASN cc_start: 0.8460 (OUTLIER) cc_final: 0.7658 (t0) REVERT: A 581 CYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7692 (t) REVERT: A 617 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7238 (tp) REVERT: A 684 MET cc_start: 0.5933 (tmm) cc_final: 0.5225 (ttm) REVERT: F 375 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8186 (mp) REVERT: F 413 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7272 (tm) REVERT: F 518 SER cc_start: 0.7697 (OUTLIER) cc_final: 0.7221 (p) REVERT: F 547 MET cc_start: 0.6913 (mpt) cc_final: 0.6434 (tmm) REVERT: F 618 MET cc_start: 0.6380 (mmt) cc_final: 0.6157 (mmm) REVERT: E 618 MET cc_start: 0.8595 (mmp) cc_final: 0.8198 (mmt) REVERT: E 636 ARG cc_start: 0.5225 (tmt90) cc_final: 0.4959 (tpt-90) outliers start: 65 outliers final: 41 residues processed: 224 average time/residue: 1.3670 time to fit residues: 344.8369 Evaluate side-chains 212 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 158 time to evaluate : 2.184 ------------------------------------------------------------------------------- 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 631 SER Chi-restraints excluded: chain C residue 649 LYS 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 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 A residue 426 MET Chi-restraints excluded: chain A residue 478 ASN 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 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 518 SER Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 436 TYR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 203 optimal weight: 2.9990 chunk 157 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 212 optimal weight: 0.4980 chunk 112 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 151 optimal weight: 0.0980 chunk 99 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 660 GLN B 529 GLN D 642 ASN A 324 ASN F 662 ASN E 660 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.146414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.107666 restraints weight = 22878.004| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.96 r_work: 0.2951 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 18487 Z= 0.181 Angle : 0.765 59.197 25020 Z= 0.426 Chirality : 0.047 1.017 2793 Planarity : 0.004 0.086 3162 Dihedral : 11.232 168.999 2571 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.53 % Allowed : 26.31 % Favored : 70.16 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.18), residues: 2195 helix: 0.61 (0.19), residues: 772 sheet: -1.07 (0.29), residues: 361 loop : -1.07 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 675 HIS 0.003 0.001 HIS D 548 PHE 0.011 0.001 PHE B 524 TYR 0.018 0.001 TYR C 606 ARG 0.019 0.001 ARG D 612 Details of bonding type rmsd hydrogen bonds : bond 0.03785 ( 547) hydrogen bonds : angle 4.17661 ( 1566) covalent geometry : bond 0.00383 (18487) covalent geometry : angle 0.76453 (25020) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13869.52 seconds wall clock time: 243 minutes 17.54 seconds (14597.54 seconds total)