Starting phenix.real_space_refine on Sun Jul 21 22:18:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj8_38396/07_2024/8xj8_38396_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj8_38396/07_2024/8xj8_38396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj8_38396/07_2024/8xj8_38396.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj8_38396/07_2024/8xj8_38396.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj8_38396/07_2024/8xj8_38396_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj8_38396/07_2024/8xj8_38396_neut.cif" } resolution = 2.67 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= -0.002 sd= 0.159 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 15 5.49 5 Mg 3 5.21 5 S 78 5.16 5 C 10127 2.51 5 N 2691 2.21 5 O 2990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 405": "OE1" <-> "OE2" Residue "A GLU 453": "OE1" <-> "OE2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A GLU 557": "OE1" <-> "OE2" Residue "B GLU 343": "OE1" <-> "OE2" Residue "B GLU 382": "OE1" <-> "OE2" Residue "B GLU 459": "OE1" <-> "OE2" Residue "B PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 405": "OE1" <-> "OE2" Residue "C GLU 459": "OE1" <-> "OE2" Residue "C GLU 474": "OE1" <-> "OE2" Residue "D GLU 453": "OE1" <-> "OE2" Residue "D PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 579": "OE1" <-> "OE2" Residue "F GLU 361": "OE1" <-> "OE2" Residue "F GLU 382": "OE1" <-> "OE2" Residue "F GLU 457": "OE1" <-> "OE2" Residue "F GLU 459": "OE1" <-> "OE2" Residue "F GLU 460": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 15904 Number of models: 1 Model: "" Number of chains: 10 Chain: "X" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "A" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3427 Classifications: {'peptide': 422} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 402} Chain breaks: 3 Chain: "B" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2990 Classifications: {'peptide': 372} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 353} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3053 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 360} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 2846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2846 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 335} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 117} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2393 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 297} Chain breaks: 4 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 70 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 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, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.70, per 1000 atoms: 0.61 Number of scatterers: 15904 At special positions: 0 Unit cell: (116.748, 124.315, 135.125, 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 78 16.00 P 15 15.00 Mg 3 11.99 O 2990 8.00 N 2691 7.00 C 10127 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 - 3.50 Amino acid : False - 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: 6.33 Conformation dependent library (CDL) restraints added in 2.8 seconds 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3744 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 25 sheets defined 42.7% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'A' and resid 324 through 335 Processing helix chain 'A' and resid 362 through 371 Processing helix chain 'A' and resid 372 through 375 Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.584A pdb=" N SER A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 385 through 400 removed outlier: 3.544A pdb=" N THR A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 removed outlier: 3.799A pdb=" N LYS A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 486 through 491 Processing helix chain 'A' and resid 508 through 521 removed outlier: 3.511A pdb=" N LYS A 513 " --> pdb=" O LYS A 509 " (cutoff:3.500A) 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: 3.749A pdb=" N ILE A 574 " --> pdb=" O ARG A 570 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A 575 " --> pdb=" O SER A 571 " (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 641 Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 664 through 680 removed outlier: 3.600A pdb=" N HIS A 680 " --> pdb=" O TYR A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 695 removed outlier: 3.707A pdb=" N ILE A 693 " --> pdb=" O PRO A 690 " (cutoff:3.500A) Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 696 through 705 removed outlier: 3.563A pdb=" N LYS A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 745 Processing helix chain 'A' and resid 752 through 762 removed outlier: 3.966A pdb=" N ILE A 756 " --> pdb=" O PHE A 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 335 Processing helix chain 'B' and resid 362 through 371 Processing helix chain 'B' and resid 372 through 375 Processing helix chain 'B' and resid 376 through 381 removed outlier: 3.654A 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: 3.505A pdb=" N THR B 391 " --> pdb=" O ARG B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.529A pdb=" N LYS B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 469 removed outlier: 4.400A pdb=" N GLU B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU B 460 " --> pdb=" O PRO B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 489 removed outlier: 3.990A pdb=" N CYS B 489 " --> pdb=" O THR B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 521 removed outlier: 3.528A pdb=" N LYS B 513 " --> pdb=" O LYS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 570 through 577 removed outlier: 3.569A pdb=" N ILE B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 619 removed outlier: 3.510A pdb=" N ARG B 619 " --> pdb=" O ASN B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' Processing helix chain 'B' and resid 635 through 640 removed outlier: 3.588A pdb=" N GLU B 640 " --> pdb=" O ARG B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 661 Processing helix chain 'B' and resid 664 through 680 Processing helix chain 'B' and resid 689 through 693 removed outlier: 3.559A pdb=" N ILE B 693 " --> pdb=" O PRO B 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 336 removed outlier: 3.782A pdb=" N THR C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 371 Processing helix chain 'C' and resid 372 through 375 removed outlier: 3.791A pdb=" N LEU C 375 " --> pdb=" O ARG C 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 372 through 375' Processing helix chain 'C' and resid 376 through 382 removed outlier: 3.816A pdb=" N SER C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 400 removed outlier: 3.502A pdb=" N LEU C 400 " --> pdb=" O ILE C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 469 removed outlier: 3.583A pdb=" N GLU C 460 " --> pdb=" O PRO C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 488 Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 510 through 521 Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 570 through 577 removed outlier: 3.804A pdb=" N ILE C 574 " --> pdb=" O ARG C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 619 Processing helix chain 'C' and resid 632 through 634 No H-bonds generated for 'chain 'C' and resid 632 through 634' Processing helix chain 'C' and resid 635 through 642 removed outlier: 3.692A pdb=" N ASN C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN C 642 " --> pdb=" O ALA C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 661 Processing helix chain 'C' and resid 664 through 680 Processing helix chain 'C' and resid 689 through 695 removed outlier: 3.531A pdb=" N GLU C 692 " --> pdb=" O THR C 689 " (cutoff:3.500A) Proline residue: C 694 - end of helix Processing helix chain 'C' and resid 696 through 702 removed outlier: 3.717A pdb=" N ILE C 702 " --> pdb=" O PHE C 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 335 Processing helix chain 'D' and resid 362 through 371 removed outlier: 3.689A pdb=" N LYS D 366 " --> pdb=" O PRO D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 375 removed outlier: 3.580A pdb=" N LEU D 375 " --> pdb=" O ARG D 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 372 through 375' Processing helix chain 'D' and resid 376 through 381 removed outlier: 3.900A pdb=" N SER D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 398 Processing helix chain 'D' and resid 432 through 436 removed outlier: 3.611A pdb=" N LYS D 435 " --> pdb=" O ASP D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 462 removed outlier: 4.566A pdb=" N MET D 458 " --> pdb=" O ASP D 454 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 469 Processing helix chain 'D' and resid 475 through 488 Processing helix chain 'D' and resid 489 through 491 No H-bonds generated for 'chain 'D' and resid 489 through 491' 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 removed outlier: 3.826A pdb=" N ILE D 574 " --> pdb=" O ARG D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 619 Processing helix chain 'D' and resid 667 through 679 Processing helix chain 'D' and resid 689 through 695 removed outlier: 3.968A pdb=" N ILE D 693 " --> pdb=" O PRO D 690 " (cutoff:3.500A) Proline residue: D 694 - end of helix Processing helix chain 'D' and resid 696 through 702 removed outlier: 3.909A pdb=" N LYS D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 335 Processing helix chain 'E' and resid 363 through 372 removed outlier: 3.734A pdb=" N ARG E 372 " --> pdb=" O ILE E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 384 removed outlier: 4.527A pdb=" N SER E 381 " --> pdb=" O GLU E 378 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU E 382 " --> pdb=" O TYR E 379 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU E 384 " --> pdb=" O SER E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 400 removed outlier: 3.505A pdb=" N ASP E 398 " --> pdb=" O ALA E 394 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU E 400 " --> pdb=" O ILE E 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 335 Processing helix chain 'F' and resid 363 through 371 Processing helix chain 'F' and resid 372 through 375 Processing helix chain 'F' and resid 376 through 381 removed outlier: 3.586A pdb=" N SER F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 384 No H-bonds generated for 'chain 'F' and resid 382 through 384' Processing helix chain 'F' and resid 385 through 400 removed outlier: 3.533A pdb=" N LEU F 400 " --> pdb=" O ILE F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 425 No H-bonds generated for 'chain 'F' and resid 423 through 425' Processing helix chain 'F' and resid 455 through 461 removed outlier: 3.881A pdb=" N GLU F 459 " --> pdb=" O SER F 455 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU F 461 " --> pdb=" O GLU F 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 468 Processing helix chain 'F' and resid 475 through 486 Processing helix chain 'F' and resid 508 through 521 removed outlier: 3.715A pdb=" N GLY F 521 " --> pdb=" O LYS F 517 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.543A pdb=" N ASP F 534 " --> pdb=" O THR F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 578 Processing helix chain 'F' and resid 665 through 677 Processing sheet with id=AA1, first strand: chain 'A' and resid 339 through 341 Processing sheet with id=AA2, first strand: chain 'A' and resid 412 through 414 Processing sheet with id=AA3, first strand: chain 'A' and resid 524 through 526 removed outlier: 6.786A pdb=" N VAL A 525 " --> pdb=" O PHE A 554 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N SER A 556 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR A 499 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N THR A 604 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N PHE A 501 " --> pdb=" O THR A 604 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU A 498 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL A 624 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N PHE A 500 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N PHE A 626 " --> pdb=" O PHE A 500 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE A 502 " --> pdb=" O PHE A 626 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 581 through 583 Processing sheet with id=AA5, first strand: chain 'A' and resid 628 through 631 removed outlier: 6.258A pdb=" N HIS A 629 " --> pdb=" O LYS A 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 706 through 707 Processing sheet with id=AA7, first strand: chain 'B' and resid 339 through 341 Processing sheet with id=AA8, first strand: chain 'B' and resid 412 through 414 Processing sheet with id=AA9, first strand: chain 'B' and resid 524 through 526 removed outlier: 6.867A pdb=" N VAL B 525 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N SER B 556 " --> pdb=" O VAL B 525 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU B 498 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL B 624 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N PHE B 626 " --> pdb=" O PHE B 500 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N PHE B 502 " --> pdb=" O PHE B 626 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AB2, first strand: chain 'B' and resid 628 through 631 removed outlier: 6.203A pdb=" N HIS B 629 " --> pdb=" O LYS B 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 339 through 341 Processing sheet with id=AB4, first strand: chain 'C' and resid 412 through 414 Processing sheet with id=AB5, first strand: chain 'C' and resid 524 through 526 removed outlier: 6.952A pdb=" N VAL C 525 " --> pdb=" O PHE C 554 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N SER C 556 " --> pdb=" O VAL C 525 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR C 499 " --> pdb=" O ILE C 602 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N THR C 604 " --> pdb=" O THR C 499 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE C 501 " --> pdb=" O THR C 604 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU C 498 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL C 624 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE C 500 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N PHE C 626 " --> pdb=" O PHE C 500 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N PHE C 502 " --> pdb=" O PHE C 626 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 581 through 583 Processing sheet with id=AB7, first strand: chain 'C' and resid 628 through 631 Processing sheet with id=AB8, first strand: chain 'D' and resid 339 through 341 removed outlier: 4.623A pdb=" N HIS D 347 " --> pdb=" O ASN D 358 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 412 through 414 Processing sheet with id=AC1, first strand: chain 'D' and resid 524 through 527 removed outlier: 6.625A pdb=" N VAL D 525 " --> pdb=" O PHE D 554 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR D 499 " --> pdb=" O ILE D 602 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N THR D 604 " --> pdb=" O THR D 499 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N PHE D 501 " --> pdb=" O THR D 604 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU D 498 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL D 624 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N PHE D 500 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N PHE D 626 " --> pdb=" O PHE D 500 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE D 502 " --> pdb=" O PHE D 626 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 581 through 583 Processing sheet with id=AC3, first strand: chain 'E' and resid 339 through 341 Processing sheet with id=AC4, first strand: chain 'E' and resid 412 through 415 Processing sheet with id=AC5, first strand: chain 'F' and resid 339 through 341 Processing sheet with id=AC6, first strand: chain 'F' and resid 412 through 415 removed outlier: 3.633A pdb=" N VAL F 419 " --> pdb=" O TYR F 428 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 524 through 525 removed outlier: 6.315A pdb=" N VAL F 553 " --> pdb=" O ILE F 601 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ASP F 603 " --> pdb=" O VAL F 553 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU F 498 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL F 624 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N PHE F 500 " --> pdb=" O VAL F 624 " (cutoff:3.500A) 510 hydrogen bonds defined for protein. 1452 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: 5.05 Time building geometry restraints manager: 6.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 2604 1.30 - 1.43: 4061 1.43 - 1.56: 9429 1.56 - 1.69: 26 1.69 - 1.82: 116 Bond restraints: 16236 Sorted by residual: bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" O3A ANP C 801 " pdb=" PB ANP C 801 " ideal model delta sigma weight residual 1.700 1.559 0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" C SER B 455 " pdb=" O SER B 455 " ideal model delta sigma weight residual 1.238 1.164 0.074 1.28e-02 6.10e+03 3.34e+01 bond pdb=" C PRO B 456 " pdb=" O PRO B 456 " ideal model delta sigma weight residual 1.238 1.174 0.065 1.22e-02 6.72e+03 2.81e+01 ... (remaining 16231 not shown) Histogram of bond angle deviations from ideal: 95.97 - 103.58: 223 103.58 - 111.18: 6390 111.18 - 118.78: 6689 118.78 - 126.39: 8459 126.39 - 133.99: 220 Bond angle restraints: 21981 Sorted by residual: angle pdb=" N PRO B 682 " pdb=" CA PRO B 682 " pdb=" CB PRO B 682 " ideal model delta sigma weight residual 103.25 112.09 -8.84 1.05e+00 9.07e-01 7.09e+01 angle pdb=" N PRO B 682 " pdb=" CA PRO B 682 " pdb=" C PRO B 682 " ideal model delta sigma weight residual 112.47 95.97 16.50 2.06e+00 2.36e-01 6.41e+01 angle pdb=" C ILE B 681 " pdb=" N PRO B 682 " pdb=" CA PRO B 682 " ideal model delta sigma weight residual 119.84 127.73 -7.89 1.25e+00 6.40e-01 3.98e+01 angle pdb=" PB ANP C 801 " pdb=" N3B ANP C 801 " pdb=" PG ANP C 801 " ideal model delta sigma weight residual 126.95 110.35 16.60 3.00e+00 1.11e-01 3.06e+01 angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 110.59 16.36 3.00e+00 1.11e-01 2.97e+01 ... (remaining 21976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.60: 8999 23.60 - 47.19: 724 47.19 - 70.79: 148 70.79 - 94.38: 30 94.38 - 117.98: 3 Dihedral angle restraints: 9904 sinusoidal: 4152 harmonic: 5752 Sorted by residual: dihedral pdb=" CA TYR F 428 " pdb=" C TYR F 428 " pdb=" N SER F 429 " pdb=" CA SER F 429 " ideal model delta harmonic sigma weight residual 180.00 -156.52 -23.48 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA LYS E 416 " pdb=" C LYS E 416 " pdb=" N ASN E 417 " pdb=" CA ASN E 417 " ideal model delta harmonic sigma weight residual 180.00 157.11 22.89 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA LYS F 678 " pdb=" C LYS F 678 " pdb=" N TYR F 679 " pdb=" CA TYR F 679 " ideal model delta harmonic sigma weight residual -180.00 -159.10 -20.90 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 9901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2183 0.062 - 0.124: 286 0.124 - 0.186: 8 0.186 - 0.248: 3 0.248 - 0.310: 5 Chirality restraints: 2485 Sorted by residual: chirality pdb=" CA ILE B 681 " pdb=" N ILE B 681 " pdb=" C ILE B 681 " pdb=" CB ILE B 681 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CB VAL F 423 " pdb=" CA VAL F 423 " pdb=" CG1 VAL F 423 " pdb=" CG2 VAL F 423 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C3' ANP C 801 " pdb=" C2' ANP C 801 " pdb=" C4' ANP C 801 " pdb=" O3' ANP C 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 2482 not shown) Planarity restraints: 2761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 450 " -0.022 2.00e-02 2.50e+03 4.26e-02 1.82e+01 pdb=" C LYS B 450 " 0.074 2.00e-02 2.50e+03 pdb=" O LYS B 450 " -0.027 2.00e-02 2.50e+03 pdb=" N PHE B 451 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 670 " -0.005 2.00e-02 2.50e+03 2.05e-02 8.41e+00 pdb=" CG TYR F 670 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR F 670 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR F 670 " -0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR F 670 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR F 670 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR F 670 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR F 670 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 421 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.73e+00 pdb=" C ASP F 421 " -0.045 2.00e-02 2.50e+03 pdb=" O ASP F 421 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU F 422 " 0.015 2.00e-02 2.50e+03 ... (remaining 2758 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 122 2.59 - 3.17: 12466 3.17 - 3.75: 23477 3.75 - 4.32: 35550 4.32 - 4.90: 56995 Nonbonded interactions: 128610 Sorted by model distance: nonbonded pdb=" O3G ANP C 801 " pdb="MG MG C 802 " model vdw 2.015 2.170 nonbonded pdb=" O2G ANP B 801 " pdb="MG MG B 802 " model vdw 2.061 2.170 nonbonded pdb=" OG SER A 510 " pdb="MG MG A 802 " model vdw 2.099 2.170 nonbonded pdb=" O2B ANP A 801 " pdb="MG MG A 802 " model vdw 2.114 2.170 nonbonded pdb=" OG SER D 359 " pdb=" OE1 GLU D 360 " model vdw 2.175 2.440 ... (remaining 128605 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 324 through 452 or (resid 453 through 455 and (name N or n \ ame CA or name C or name O or name CB )) or resid 456 through 636 or (resid 637 \ through 641 and (name N or name CA or name C or name O or name CB )) or resid 64 \ 2 through 681 or (resid 682 and (name N or name CA or name C or name O or name C \ B )) or resid 683 through 695 or resid 801 through 802)) selection = (chain 'B' and (resid 324 through 484 or resid 486 through 636 or (resid 637 thr \ ough 641 and (name N or name CA or name C or name O or name CB )) or resid 642 t \ hrough 695 or resid 801 through 802)) selection = (chain 'C' and (resid 324 through 452 or (resid 453 through 455 and (name N or n \ ame CA or name C or name O or name CB )) or resid 456 through 484 or resid 486 t \ hrough 681 or (resid 682 and (name N or name CA or name C or name O or name CB ) \ ) or resid 683 through 695 or resid 801 through 802)) } ncs_group { reference = (chain 'D' and (resid 324 through 423 or (resid 424 and (name N or name CA or na \ me C or name O or name CB )) or resid 425 or (resid 426 and (name N or name CA o \ r name C or name O or name CB )) or resid 427 through 473 or (resid 474 and (nam \ e N or name CA or name C or name O or name CB )) or resid 475 or (resid 476 thro \ ugh 477 and (name N or name CA or name C or name O or name CB )) or resid 478 th \ rough 503 or (resid 504 and (name N or name CA or name C or name O or name CB )) \ or resid 505 through 528 or (resid 529 and (name N or name CA or name C or name \ O or name CB )) or resid 530 through 533 or (resid 534 and (name N or name CA o \ r name C or name O or name CB )) or resid 543 through 557 or (resid 558 and (nam \ e N or name CA or name C or name O or name CB )) or resid 559 through 561 or (re \ sid 567 through 568 and (name N or name CA or name C or name O or name CB )) or \ resid 569 or (resid 570 and (name N or name CA or name C or name O or name CB )) \ or resid 571 or (resid 572 and (name N or name CA or name C or name O or name C \ B )) or resid 573 through 574 or (resid 575 through 576 and (name N or name CA o \ r name C or name O or name CB )) or resid 577 or (resid 578 through 579 and (nam \ e N or name CA or name C or name O or name CB )) or resid 596 through 611 or (re \ sid 612 and (name N or name CA or name C or name O or name CB )) or resid 613 or \ (resid 614 through 620 and (name N or name CA or name C or name O or name CB )) \ or resid 621 through 624 or (resid 625 and (name N or name CA or name C or name \ O or name CB )) or resid 626 or (resid 627 and (name N or name CA or name C or \ name O or name CB )) or resid 628 or (resid 629 and (name N or name CA or name C \ or name O or name CB )) or resid 655 through 684)) selection = (chain 'F' and (resid 324 through 559 or (resid 560 and (name N or name CA or na \ me C or name O or name CB )) or resid 561 or resid 567 through 684)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 45.720 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.080 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:12.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3505 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 0.142 16236 Z= 0.284 Angle : 0.732 16.602 21981 Z= 0.394 Chirality : 0.044 0.310 2485 Planarity : 0.004 0.057 2761 Dihedral : 17.643 117.981 6160 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.73 % Allowed : 4.00 % Favored : 95.28 % Rotamer: Outliers : 2.00 % Allowed : 16.35 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % 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: -0.63 (0.19), residues: 1927 helix: -0.02 (0.20), residues: 678 sheet: -0.19 (0.34), residues: 283 loop : -0.69 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 350 HIS 0.006 0.001 HIS B 680 PHE 0.023 0.001 PHE B 451 TYR 0.045 0.001 TYR F 670 ARG 0.016 0.000 ARG D 625 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 274 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 574 ILE cc_start: 0.5818 (mm) cc_final: 0.5519 (mm) REVERT: B 415 PHE cc_start: 0.5596 (m-80) cc_final: 0.5367 (m-80) REVERT: B 432 ASP cc_start: 0.2521 (OUTLIER) cc_final: 0.2199 (t70) REVERT: C 547 MET cc_start: 0.4147 (mtm) cc_final: 0.3850 (pp-130) REVERT: D 495 LYS cc_start: 0.6093 (mppt) cc_final: 0.5531 (mmtt) REVERT: D 502 PHE cc_start: 0.4751 (t80) cc_final: 0.4543 (t80) REVERT: D 571 SER cc_start: 0.6315 (m) cc_final: 0.5952 (p) REVERT: E 354 SER cc_start: 0.5654 (t) cc_final: 0.5320 (t) REVERT: E 422 LEU cc_start: 0.3097 (OUTLIER) cc_final: 0.2726 (tt) REVERT: E 444 PHE cc_start: 0.5475 (OUTLIER) cc_final: 0.5252 (p90) REVERT: F 354 SER cc_start: 0.4768 (t) cc_final: 0.4468 (t) REVERT: F 366 LYS cc_start: 0.7116 (mttt) cc_final: 0.6515 (mtpp) REVERT: F 413 LEU cc_start: 0.5054 (mt) cc_final: 0.4801 (mt) REVERT: F 423 VAL cc_start: 0.5991 (p) cc_final: 0.5737 (m) REVERT: F 465 ILE cc_start: 0.3814 (pp) cc_final: 0.3371 (mt) outliers start: 35 outliers final: 7 residues processed: 304 average time/residue: 1.0975 time to fit residues: 374.3082 Evaluate side-chains 158 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 148 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 444 PHE Chi-restraints excluded: chain F residue 556 SER Chi-restraints excluded: chain F residue 679 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 3.9990 chunk 147 optimal weight: 0.3980 chunk 81 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 113 optimal weight: 0.2980 chunk 176 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 HIS A 374 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN A 629 HIS A 641 ASN A 680 HIS B 596 ASN B 605 ASN ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 546 ASN C 548 HIS C 597 HIS D 548 HIS D 593 ASN D 661 ASN F 478 ASN F 546 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.7159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 16236 Z= 0.334 Angle : 0.847 14.600 21981 Z= 0.439 Chirality : 0.050 0.303 2485 Planarity : 0.006 0.071 2761 Dihedral : 10.814 151.131 2278 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.46 % Favored : 95.07 % Rotamer: Outliers : 5.20 % Allowed : 17.95 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.06 (0.19), residues: 1927 helix: -0.51 (0.18), residues: 708 sheet: -0.53 (0.31), residues: 303 loop : -0.79 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP F 350 HIS 0.013 0.002 HIS F 680 PHE 0.035 0.003 PHE F 427 TYR 0.025 0.002 TYR F 670 ARG 0.034 0.001 ARG A 570 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 355 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 PHE cc_start: 0.5144 (OUTLIER) cc_final: 0.3921 (m-80) REVERT: A 495 LYS cc_start: 0.7052 (mppt) cc_final: 0.6740 (mptt) REVERT: B 380 SER cc_start: 0.7375 (p) cc_final: 0.7151 (t) REVERT: B 387 ARG cc_start: 0.6522 (OUTLIER) cc_final: 0.5993 (ptt-90) REVERT: B 593 ASN cc_start: 0.8457 (p0) cc_final: 0.8062 (p0) REVERT: B 615 ASN cc_start: 0.6837 (m-40) cc_final: 0.6617 (m110) REVERT: C 360 GLU cc_start: 0.6072 (pm20) cc_final: 0.5850 (pm20) REVERT: C 377 LYS cc_start: 0.7290 (ttpp) cc_final: 0.6895 (mmtm) REVERT: C 578 THR cc_start: 0.7772 (OUTLIER) cc_final: 0.7515 (p) REVERT: D 356 LYS cc_start: 0.6278 (mttt) cc_final: 0.6065 (mtmm) REVERT: D 435 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7598 (pttm) REVERT: D 500 PHE cc_start: 0.7188 (m-80) cc_final: 0.6810 (m-10) REVERT: D 684 MET cc_start: 0.4964 (OUTLIER) cc_final: 0.4393 (ptt) REVERT: F 413 LEU cc_start: 0.6517 (mt) cc_final: 0.6309 (mt) REVERT: F 420 LEU cc_start: 0.6616 (tp) cc_final: 0.6329 (tm) REVERT: F 457 GLU cc_start: 0.6079 (mm-30) cc_final: 0.5103 (mp0) REVERT: F 465 ILE cc_start: 0.4833 (pp) cc_final: 0.4184 (mt) REVERT: F 467 ASP cc_start: 0.2421 (OUTLIER) cc_final: 0.2061 (t70) REVERT: F 556 SER cc_start: 0.5338 (p) cc_final: 0.4798 (t) REVERT: F 665 ARG cc_start: 0.4824 (OUTLIER) cc_final: 0.4480 (ttm170) REVERT: F 679 TYR cc_start: 0.4902 (OUTLIER) cc_final: 0.4172 (m-80) outliers start: 91 outliers final: 21 residues processed: 414 average time/residue: 1.2548 time to fit residues: 573.1641 Evaluate side-chains 247 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 218 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 PHE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 387 ARG Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 467 ASP Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 665 ARG Chi-restraints excluded: chain F residue 679 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 146 optimal weight: 0.6980 chunk 119 optimal weight: 8.9990 chunk 48 optimal weight: 0.0070 chunk 176 optimal weight: 1.9990 chunk 190 optimal weight: 0.0060 chunk 157 optimal weight: 1.9990 chunk 175 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 overall best weight: 0.6816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN A 475 ASN A 541 ASN A 596 ASN A 597 HIS B 629 HIS C 573 ASN C 593 ASN C 596 ASN ** D 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 529 GLN D 548 HIS D 615 ASN E 395 ASN F 352 ASN ** F 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 1.0170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 16236 Z= 0.231 Angle : 0.648 19.267 21981 Z= 0.335 Chirality : 0.045 0.465 2485 Planarity : 0.005 0.052 2761 Dihedral : 9.928 148.663 2263 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.05 % Favored : 95.54 % Rotamer: Outliers : 5.03 % Allowed : 20.13 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % 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: -0.59 (0.19), residues: 1927 helix: 0.31 (0.19), residues: 730 sheet: -0.44 (0.35), residues: 244 loop : -0.86 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 355 HIS 0.005 0.001 HIS B 597 PHE 0.017 0.002 PHE F 427 TYR 0.019 0.002 TYR B 482 ARG 0.004 0.001 ARG F 665 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 283 time to evaluate : 1.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7430 (mt0) REVERT: A 526 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7766 (tm-30) REVERT: B 526 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7928 (tp30) REVERT: B 547 MET cc_start: 0.8056 (ptm) cc_final: 0.7764 (mtp) REVERT: B 663 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7667 (ttt-90) REVERT: C 387 ARG cc_start: 0.7273 (mtm180) cc_final: 0.7010 (mtt180) REVERT: C 544 ILE cc_start: 0.8657 (mm) cc_final: 0.8438 (mm) REVERT: C 547 MET cc_start: 0.8403 (mtp) cc_final: 0.8169 (mtm) REVERT: C 600 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8107 (mm) REVERT: C 684 MET cc_start: 0.6299 (OUTLIER) cc_final: 0.5884 (ttp) REVERT: D 390 LYS cc_start: 0.8937 (mttm) cc_final: 0.8736 (mmpt) REVERT: D 426 MET cc_start: 0.5865 (OUTLIER) cc_final: 0.5581 (mmt) REVERT: D 484 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7696 (tttm) REVERT: D 543 PHE cc_start: 0.6129 (m-10) cc_final: 0.5927 (m-80) REVERT: D 677 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8178 (tppt) REVERT: E 341 LEU cc_start: 0.6608 (OUTLIER) cc_final: 0.6332 (tp) REVERT: E 374 GLN cc_start: 0.7420 (mt0) cc_final: 0.7110 (mp10) REVERT: F 465 ILE cc_start: 0.4370 (OUTLIER) cc_final: 0.4012 (mt) REVERT: F 555 CYS cc_start: 0.5312 (OUTLIER) cc_final: 0.3871 (p) outliers start: 88 outliers final: 19 residues processed: 342 average time/residue: 1.4152 time to fit residues: 529.6546 Evaluate side-chains 245 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 214 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 663 ARG Chi-restraints excluded: chain B residue 680 HIS Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 484 LYS Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 677 LYS Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 465 ILE Chi-restraints excluded: chain F residue 512 THR Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 555 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 174 optimal weight: 0.0670 chunk 132 optimal weight: 0.3980 chunk 91 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 84 optimal weight: 0.0060 chunk 118 optimal weight: 7.9990 chunk 177 optimal weight: 7.9990 chunk 187 optimal weight: 20.0000 chunk 92 optimal weight: 0.7980 chunk 167 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 ASN C 593 ASN C 661 ASN ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 HIS D 597 HIS F 347 HIS F 374 GLN F 475 ASN F 478 ASN F 680 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 1.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.092 16236 Z= 0.155 Angle : 0.535 13.013 21981 Z= 0.280 Chirality : 0.041 0.136 2485 Planarity : 0.004 0.041 2761 Dihedral : 9.446 144.898 2261 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.79 % Favored : 95.80 % Rotamer: Outliers : 4.06 % Allowed : 22.18 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % 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: -0.21 (0.19), residues: 1927 helix: 0.68 (0.20), residues: 723 sheet: -0.36 (0.34), residues: 265 loop : -0.66 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 675 HIS 0.003 0.001 HIS D 597 PHE 0.014 0.001 PHE F 415 TYR 0.012 0.001 TYR F 670 ARG 0.006 0.000 ARG D 663 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 262 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7450 (mt0) REVERT: A 399 MET cc_start: 0.9018 (mtt) cc_final: 0.8612 (mtt) REVERT: A 448 ASP cc_start: 0.6947 (OUTLIER) cc_final: 0.6662 (m-30) REVERT: A 462 MET cc_start: 0.9130 (mmm) cc_final: 0.8725 (mmt) REVERT: B 357 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7591 (t80) REVERT: B 547 MET cc_start: 0.8304 (ptm) cc_final: 0.7992 (ptm) REVERT: C 387 ARG cc_start: 0.7143 (mtm180) cc_final: 0.6802 (mtp180) REVERT: C 426 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7457 (mtm) REVERT: C 476 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8553 (tmtm) REVERT: C 579 GLU cc_start: 0.8267 (mm-30) cc_final: 0.8041 (mm-30) REVERT: C 677 LYS cc_start: 0.7764 (mmpt) cc_final: 0.7461 (mtmm) REVERT: D 579 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7330 (mm-30) REVERT: D 591 LYS cc_start: 0.8359 (mmtp) cc_final: 0.8077 (mmtm) REVERT: E 341 LEU cc_start: 0.6702 (OUTLIER) cc_final: 0.6472 (tp) REVERT: E 426 MET cc_start: 0.4286 (tpp) cc_final: 0.4034 (ppp) REVERT: F 465 ILE cc_start: 0.4589 (OUTLIER) cc_final: 0.4233 (mt) REVERT: F 467 ASP cc_start: 0.3190 (OUTLIER) cc_final: 0.2495 (t70) REVERT: F 510 SER cc_start: 0.7193 (m) cc_final: 0.6635 (t) REVERT: F 555 CYS cc_start: 0.5132 (OUTLIER) cc_final: 0.3925 (p) REVERT: F 674 LYS cc_start: 0.7236 (mmmm) cc_final: 0.6943 (mtpm) outliers start: 71 outliers final: 20 residues processed: 301 average time/residue: 1.5059 time to fit residues: 493.3937 Evaluate side-chains 254 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 225 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 465 ILE Chi-restraints excluded: chain F residue 467 ASP Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 571 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 156 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 139 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 HIS C 593 ASN ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 1.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16236 Z= 0.178 Angle : 0.560 11.978 21981 Z= 0.295 Chirality : 0.042 0.168 2485 Planarity : 0.004 0.048 2761 Dihedral : 9.486 143.764 2261 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.84 % Favored : 95.74 % Rotamer: Outliers : 4.12 % Allowed : 22.53 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % 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: -0.09 (0.19), residues: 1927 helix: 0.84 (0.20), residues: 738 sheet: -0.35 (0.36), residues: 235 loop : -0.64 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 355 HIS 0.006 0.001 HIS B 597 PHE 0.015 0.001 PHE F 427 TYR 0.017 0.001 TYR B 482 ARG 0.007 0.000 ARG D 625 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 282 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ARG cc_start: 0.8576 (mtt180) cc_final: 0.8312 (mtp180) REVERT: A 372 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8136 (ttp80) REVERT: A 448 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.6944 (m-30) REVERT: A 462 MET cc_start: 0.9258 (mmm) cc_final: 0.8890 (mmt) REVERT: B 357 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.7868 (t80) REVERT: B 387 ARG cc_start: 0.7535 (ttp-170) cc_final: 0.6979 (mtt90) REVERT: B 526 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7883 (tm-30) REVERT: B 547 MET cc_start: 0.8378 (ptm) cc_final: 0.8074 (ptm) REVERT: B 606 TYR cc_start: 0.8783 (m-80) cc_final: 0.8482 (m-80) REVERT: C 387 ARG cc_start: 0.7377 (mtm180) cc_final: 0.6844 (mtp180) REVERT: C 618 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.7345 (mpp) REVERT: D 424 ASP cc_start: 0.7552 (t70) cc_final: 0.7211 (t0) REVERT: D 445 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7584 (ttpt) REVERT: D 534 ASP cc_start: 0.7662 (m-30) cc_final: 0.7391 (m-30) REVERT: D 570 ARG cc_start: 0.7517 (ttm-80) cc_final: 0.7261 (ttm-80) REVERT: D 579 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7583 (mm-30) REVERT: D 591 LYS cc_start: 0.8432 (mmtp) cc_final: 0.8165 (mmtm) REVERT: D 625 ARG cc_start: 0.7195 (ptt90) cc_final: 0.6760 (mtp85) REVERT: F 374 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7702 (mt0) REVERT: F 416 LYS cc_start: 0.6956 (tmmm) cc_final: 0.6728 (tmmm) REVERT: F 467 ASP cc_start: 0.3701 (OUTLIER) cc_final: 0.2557 (t70) REVERT: F 502 PHE cc_start: 0.5854 (OUTLIER) cc_final: 0.4643 (t80) REVERT: F 555 CYS cc_start: 0.4482 (OUTLIER) cc_final: 0.3989 (p) outliers start: 72 outliers final: 26 residues processed: 321 average time/residue: 1.4299 time to fit residues: 501.0425 Evaluate side-chains 270 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 234 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 378 GLU Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 445 LYS Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 374 GLN Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 436 TYR Chi-restraints excluded: chain F residue 467 ASP Chi-restraints excluded: chain F residue 502 PHE Chi-restraints excluded: chain F residue 512 THR Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 547 MET Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 571 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 63 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 187 optimal weight: 20.0000 chunk 155 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN A 629 HIS C 593 ASN C 661 ASN D 548 HIS F 596 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 1.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16236 Z= 0.224 Angle : 0.594 12.285 21981 Z= 0.312 Chirality : 0.044 0.201 2485 Planarity : 0.004 0.046 2761 Dihedral : 9.714 138.213 2261 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.94 % Favored : 95.64 % Rotamer: Outliers : 4.63 % Allowed : 21.27 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % 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: -0.16 (0.19), residues: 1927 helix: 0.72 (0.19), residues: 726 sheet: -0.12 (0.39), residues: 213 loop : -0.68 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 355 HIS 0.007 0.001 HIS B 597 PHE 0.013 0.002 PHE A 524 TYR 0.022 0.002 TYR E 428 ARG 0.008 0.001 ARG D 663 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 258 time to evaluate : 1.900 Fit side-chains revert: symmetry clash REVERT: A 332 ARG cc_start: 0.8529 (mtt180) cc_final: 0.8235 (mtp180) REVERT: A 343 GLU cc_start: 0.7880 (mp0) cc_final: 0.7558 (mp0) REVERT: A 372 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8244 (ttp80) REVERT: A 399 MET cc_start: 0.9155 (mtt) cc_final: 0.8794 (mtt) REVERT: A 405 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7551 (mm-30) REVERT: A 476 LYS cc_start: 0.8446 (tmmt) cc_final: 0.7985 (ttmt) REVERT: B 356 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8376 (mttm) REVERT: B 357 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.8211 (t80) REVERT: B 526 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7922 (tm-30) REVERT: B 529 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7623 (pp30) REVERT: B 547 MET cc_start: 0.8343 (ptm) cc_final: 0.8060 (ptm) REVERT: B 619 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7688 (mtp85) REVERT: C 343 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7916 (mm-30) REVERT: C 387 ARG cc_start: 0.7549 (mtm180) cc_final: 0.6826 (mtp180) REVERT: C 448 ASP cc_start: 0.7711 (p0) cc_final: 0.7455 (p0) REVERT: C 568 LYS cc_start: 0.8364 (mmtt) cc_final: 0.8124 (mmtp) REVERT: C 618 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8550 (mtm) REVERT: C 660 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8280 (tt0) REVERT: D 424 ASP cc_start: 0.7613 (t70) cc_final: 0.7151 (t0) REVERT: D 445 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7788 (ttpt) REVERT: D 458 MET cc_start: 0.4873 (tpt) cc_final: 0.4408 (tpt) REVERT: D 543 PHE cc_start: 0.6753 (m-10) cc_final: 0.6462 (m-80) REVERT: D 570 ARG cc_start: 0.7695 (ttm-80) cc_final: 0.7218 (ttm-80) REVERT: D 591 LYS cc_start: 0.8514 (mmtp) cc_final: 0.8257 (mmtm) REVERT: D 625 ARG cc_start: 0.7224 (ptt90) cc_final: 0.6950 (mtm-85) REVERT: D 628 THR cc_start: 0.6477 (OUTLIER) cc_final: 0.6088 (m) REVERT: E 332 ARG cc_start: 0.7487 (mtt-85) cc_final: 0.7266 (mtp85) REVERT: E 428 TYR cc_start: 0.5698 (OUTLIER) cc_final: 0.5223 (m-10) REVERT: F 374 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7672 (mt0) REVERT: F 416 LYS cc_start: 0.7232 (tmmm) cc_final: 0.6860 (tmmm) REVERT: F 461 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.6792 (mt) REVERT: F 517 LYS cc_start: 0.6614 (tptt) cc_final: 0.6373 (tptt) outliers start: 81 outliers final: 23 residues processed: 307 average time/residue: 1.4267 time to fit residues: 478.4609 Evaluate side-chains 272 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 235 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 680 HIS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 619 ARG Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 445 LYS Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 428 TYR Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 374 GLN Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 512 THR Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 571 SER Chi-restraints excluded: chain F residue 604 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 180 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 106 optimal weight: 0.0370 chunk 137 optimal weight: 9.9990 chunk 158 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 chunk 117 optimal weight: 1.9990 chunk 113 optimal weight: 0.0670 chunk 86 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 352 ASN C 593 ASN D 529 GLN D 548 HIS D 596 ASN D 605 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 1.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16236 Z= 0.214 Angle : 0.566 12.884 21981 Z= 0.297 Chirality : 0.043 0.149 2485 Planarity : 0.004 0.052 2761 Dihedral : 9.696 139.768 2261 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.10 % Favored : 95.49 % Rotamer: Outliers : 3.09 % Allowed : 23.21 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % 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: -0.01 (0.19), residues: 1927 helix: 0.84 (0.20), residues: 724 sheet: 0.04 (0.37), residues: 235 loop : -0.62 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 355 HIS 0.007 0.001 HIS B 597 PHE 0.013 0.002 PHE A 524 TYR 0.025 0.002 TYR F 670 ARG 0.008 0.001 ARG D 663 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 260 time to evaluate : 1.906 Fit side-chains revert: symmetry clash REVERT: A 332 ARG cc_start: 0.8517 (mtt180) cc_final: 0.8243 (mtp180) REVERT: A 360 GLU cc_start: 0.7570 (mp0) cc_final: 0.7076 (pm20) REVERT: A 372 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8571 (ttp-170) REVERT: A 399 MET cc_start: 0.9061 (mtt) cc_final: 0.8744 (mtt) REVERT: A 476 LYS cc_start: 0.8441 (tmmt) cc_final: 0.8018 (ttmt) REVERT: A 685 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.7140 (ptmt) REVERT: B 356 LYS cc_start: 0.8992 (ptpp) cc_final: 0.8495 (mttm) REVERT: B 357 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.8259 (t80) REVERT: B 526 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7948 (tm-30) REVERT: B 529 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.7548 (pp30) REVERT: B 547 MET cc_start: 0.8350 (ptm) cc_final: 0.8064 (ptm) REVERT: B 568 LYS cc_start: 0.8546 (mmtt) cc_final: 0.8219 (mmtm) REVERT: C 387 ARG cc_start: 0.7575 (mtm180) cc_final: 0.6850 (mtp180) REVERT: C 448 ASP cc_start: 0.7806 (p0) cc_final: 0.7562 (p0) REVERT: C 568 LYS cc_start: 0.8403 (mmtt) cc_final: 0.8123 (mmtp) REVERT: D 445 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7764 (ttpt) REVERT: D 517 LYS cc_start: 0.8320 (tptm) cc_final: 0.7646 (tppt) REVERT: D 543 PHE cc_start: 0.6781 (m-10) cc_final: 0.6491 (m-80) REVERT: D 570 ARG cc_start: 0.7472 (ttm-80) cc_final: 0.7207 (ttm-80) REVERT: D 591 LYS cc_start: 0.8502 (mmtp) cc_final: 0.8250 (mmtm) REVERT: D 628 THR cc_start: 0.6649 (OUTLIER) cc_final: 0.6351 (m) REVERT: E 402 ASP cc_start: 0.7344 (OUTLIER) cc_final: 0.6347 (m-30) REVERT: E 428 TYR cc_start: 0.5690 (OUTLIER) cc_final: 0.4688 (m-10) REVERT: F 374 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7723 (mt0) REVERT: F 416 LYS cc_start: 0.7646 (tmmm) cc_final: 0.7290 (tmmm) REVERT: F 461 LEU cc_start: 0.7162 (pt) cc_final: 0.6693 (mt) REVERT: F 604 THR cc_start: 0.5905 (OUTLIER) cc_final: 0.5446 (t) outliers start: 54 outliers final: 26 residues processed: 296 average time/residue: 1.4166 time to fit residues: 458.7934 Evaluate side-chains 274 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 237 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 680 HIS Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 445 LYS Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 428 TYR Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 374 GLN Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain F residue 512 THR Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 571 SER Chi-restraints excluded: chain F residue 604 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 74 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 146 optimal weight: 7.9990 chunk 170 optimal weight: 0.7980 chunk 179 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 629 HIS C 593 ASN D 548 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 1.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16236 Z= 0.237 Angle : 0.592 12.027 21981 Z= 0.309 Chirality : 0.044 0.162 2485 Planarity : 0.004 0.055 2761 Dihedral : 9.711 137.407 2261 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.84 % Favored : 95.69 % Rotamer: Outliers : 3.32 % Allowed : 23.56 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % 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: -0.08 (0.19), residues: 1927 helix: 0.69 (0.19), residues: 731 sheet: 0.02 (0.37), residues: 235 loop : -0.58 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 675 HIS 0.010 0.001 HIS B 597 PHE 0.016 0.002 PHE E 427 TYR 0.019 0.002 TYR B 482 ARG 0.008 0.001 ARG F 665 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 251 time to evaluate : 1.818 Fit side-chains REVERT: A 332 ARG cc_start: 0.8515 (mtt180) cc_final: 0.8215 (mtp180) REVERT: A 343 GLU cc_start: 0.7941 (mp0) cc_final: 0.7620 (mp0) REVERT: A 360 GLU cc_start: 0.7570 (mp0) cc_final: 0.7101 (pm20) REVERT: A 372 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8587 (ttp-170) REVERT: A 399 MET cc_start: 0.9101 (mtt) cc_final: 0.8772 (mtt) REVERT: A 405 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7431 (mm-30) REVERT: A 476 LYS cc_start: 0.8436 (tmmt) cc_final: 0.8017 (ttmt) REVERT: A 566 SER cc_start: 0.7738 (t) cc_final: 0.7443 (m) REVERT: A 614 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7473 (p0) REVERT: A 637 GLU cc_start: 0.5988 (mm-30) cc_final: 0.5700 (mp0) REVERT: A 656 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.6922 (m-30) REVERT: A 685 LYS cc_start: 0.7487 (mmmt) cc_final: 0.7169 (ptmt) REVERT: B 356 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8438 (ptpp) REVERT: B 357 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.8309 (t80) REVERT: B 526 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7947 (tm-30) REVERT: B 529 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.7618 (pp30) REVERT: B 547 MET cc_start: 0.8419 (ptm) cc_final: 0.8151 (ptm) REVERT: B 568 LYS cc_start: 0.8536 (mmtt) cc_final: 0.8240 (mmtm) REVERT: C 448 ASP cc_start: 0.7794 (p0) cc_final: 0.7570 (p0) REVERT: C 568 LYS cc_start: 0.8387 (mmtt) cc_final: 0.8108 (mmtp) REVERT: C 660 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8206 (tt0) REVERT: D 445 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7791 (ttpt) REVERT: D 543 PHE cc_start: 0.6627 (m-10) cc_final: 0.6362 (m-80) REVERT: D 570 ARG cc_start: 0.7441 (ttm-80) cc_final: 0.7176 (ttt90) REVERT: D 591 LYS cc_start: 0.8534 (mmtp) cc_final: 0.8285 (mmtm) REVERT: F 346 ASP cc_start: 0.7522 (p0) cc_final: 0.7216 (p0) REVERT: F 374 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7762 (mt0) REVERT: F 416 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.7089 (tmmm) REVERT: F 461 LEU cc_start: 0.7226 (pt) cc_final: 0.6795 (mt) REVERT: F 499 THR cc_start: 0.5577 (m) cc_final: 0.5347 (p) REVERT: F 552 SER cc_start: 0.7239 (t) cc_final: 0.6983 (p) REVERT: F 604 THR cc_start: 0.5835 (p) cc_final: 0.5443 (t) outliers start: 58 outliers final: 27 residues processed: 286 average time/residue: 1.4648 time to fit residues: 457.5663 Evaluate side-chains 271 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 232 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 612 ARG Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 680 HIS Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 445 LYS Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 374 GLN Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain F residue 416 LYS Chi-restraints excluded: chain F residue 512 THR Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 571 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 9.9990 chunk 174 optimal weight: 4.9990 chunk 179 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 136 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 173 optimal weight: 0.0980 chunk 114 optimal weight: 3.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 761 ASN C 546 ASN C 593 ASN ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 HIS E 358 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 1.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 16236 Z= 0.439 Angle : 0.740 10.290 21981 Z= 0.384 Chirality : 0.050 0.231 2485 Planarity : 0.005 0.059 2761 Dihedral : 10.762 135.569 2261 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.98 % Favored : 94.55 % Rotamer: Outliers : 3.14 % Allowed : 23.84 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % 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: -0.52 (0.19), residues: 1927 helix: 0.25 (0.19), residues: 716 sheet: -0.25 (0.33), residues: 267 loop : -0.76 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP F 675 HIS 0.015 0.002 HIS B 597 PHE 0.025 0.003 PHE E 427 TYR 0.025 0.002 TYR B 679 ARG 0.009 0.001 ARG B 665 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 253 time to evaluate : 1.926 Fit side-chains REVERT: A 332 ARG cc_start: 0.8538 (mtt180) cc_final: 0.8237 (mtp180) REVERT: A 343 GLU cc_start: 0.7987 (mp0) cc_final: 0.7615 (mp0) REVERT: A 360 GLU cc_start: 0.7470 (mp0) cc_final: 0.7004 (mp0) REVERT: A 372 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8702 (ttp-170) REVERT: A 405 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7427 (mm-30) REVERT: A 476 LYS cc_start: 0.8388 (tmmt) cc_final: 0.7976 (ttmt) REVERT: A 614 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7451 (p0) REVERT: A 637 GLU cc_start: 0.6105 (mm-30) cc_final: 0.5836 (mp0) REVERT: A 656 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.6898 (m-30) REVERT: A 685 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.6880 (mmmt) REVERT: B 356 LYS cc_start: 0.9089 (ptpp) cc_final: 0.8817 (ptmt) REVERT: B 357 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.8409 (t80) REVERT: B 426 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7970 (ttm) REVERT: B 526 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7841 (tm-30) REVERT: B 547 MET cc_start: 0.8485 (ptm) cc_final: 0.8168 (ptm) REVERT: C 448 ASP cc_start: 0.7784 (p0) cc_final: 0.7494 (p0) REVERT: C 529 GLN cc_start: 0.8311 (pt0) cc_final: 0.7906 (pp30) REVERT: C 568 LYS cc_start: 0.8303 (mmtt) cc_final: 0.7943 (mmmm) REVERT: D 374 GLN cc_start: 0.7502 (mt0) cc_final: 0.7277 (mt0) REVERT: D 445 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7703 (ttpt) REVERT: D 447 ASP cc_start: 0.7561 (t0) cc_final: 0.6695 (m-30) REVERT: D 543 PHE cc_start: 0.6734 (m-10) cc_final: 0.6468 (m-80) REVERT: D 570 ARG cc_start: 0.7323 (ttm-80) cc_final: 0.7100 (ttm-80) REVERT: D 591 LYS cc_start: 0.8532 (mmtp) cc_final: 0.8310 (mmtm) REVERT: D 603 ASP cc_start: 0.7753 (m-30) cc_final: 0.7509 (t70) REVERT: D 609 VAL cc_start: 0.8197 (t) cc_final: 0.7808 (p) REVERT: D 627 ARG cc_start: 0.6968 (ptp-110) cc_final: 0.6675 (ttp-110) REVERT: F 374 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7697 (mt0) REVERT: F 416 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7570 (tmmm) REVERT: F 461 LEU cc_start: 0.7334 (pt) cc_final: 0.7031 (mt) REVERT: F 469 GLN cc_start: 0.5084 (mm-40) cc_final: 0.4565 (mm110) REVERT: F 499 THR cc_start: 0.6018 (m) cc_final: 0.5797 (p) REVERT: F 551 ARG cc_start: 0.5677 (mmt90) cc_final: 0.5394 (mmt90) REVERT: F 552 SER cc_start: 0.7532 (t) cc_final: 0.7274 (p) REVERT: F 555 CYS cc_start: 0.6238 (OUTLIER) cc_final: 0.4920 (t) REVERT: F 604 THR cc_start: 0.5848 (p) cc_final: 0.5551 (t) outliers start: 55 outliers final: 28 residues processed: 289 average time/residue: 1.4379 time to fit residues: 454.6712 Evaluate side-chains 277 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 237 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 680 HIS Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 612 ARG Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 445 LYS Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 374 GLN Chi-restraints excluded: chain F residue 416 LYS Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 571 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 184 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 193 optimal weight: 0.8980 chunk 177 optimal weight: 10.0000 chunk 153 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 122 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 593 ASN ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 1.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16236 Z= 0.164 Angle : 0.557 12.046 21981 Z= 0.292 Chirality : 0.042 0.159 2485 Planarity : 0.004 0.060 2761 Dihedral : 9.596 138.147 2261 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.48 % Favored : 96.11 % Rotamer: Outliers : 1.94 % Allowed : 25.39 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % 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: -0.10 (0.19), residues: 1927 helix: 0.74 (0.20), residues: 709 sheet: -0.05 (0.38), residues: 231 loop : -0.61 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 675 HIS 0.005 0.001 HIS B 597 PHE 0.014 0.001 PHE F 427 TYR 0.016 0.001 TYR B 482 ARG 0.008 0.000 ARG D 663 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 251 time to evaluate : 2.250 Fit side-chains REVERT: A 332 ARG cc_start: 0.8509 (mtt180) cc_final: 0.8210 (mtp180) REVERT: A 360 GLU cc_start: 0.7527 (mp0) cc_final: 0.7106 (pm20) REVERT: A 372 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8553 (ttp-170) REVERT: A 399 MET cc_start: 0.9129 (mtt) cc_final: 0.8819 (mtt) REVERT: A 476 LYS cc_start: 0.8376 (tmmt) cc_final: 0.7993 (ttmt) REVERT: A 614 ASP cc_start: 0.7833 (OUTLIER) cc_final: 0.7485 (p0) REVERT: A 637 GLU cc_start: 0.6234 (mm-30) cc_final: 0.5954 (mp0) REVERT: A 656 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.7024 (m-30) REVERT: B 372 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8425 (ttp80) REVERT: B 526 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7809 (tm-30) REVERT: B 529 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7509 (pp30) REVERT: B 547 MET cc_start: 0.8324 (ptm) cc_final: 0.8035 (ptm) REVERT: C 387 ARG cc_start: 0.7604 (mtm180) cc_final: 0.6852 (mtp180) REVERT: C 448 ASP cc_start: 0.7813 (p0) cc_final: 0.7586 (p0) REVERT: C 529 GLN cc_start: 0.8175 (pt0) cc_final: 0.7787 (pp30) REVERT: C 568 LYS cc_start: 0.8149 (mmtt) cc_final: 0.7872 (mmmm) REVERT: D 447 ASP cc_start: 0.7268 (t0) cc_final: 0.6280 (m-30) REVERT: D 578 THR cc_start: 0.8325 (m) cc_final: 0.8015 (p) REVERT: D 591 LYS cc_start: 0.8451 (mmtp) cc_final: 0.8247 (mmtm) REVERT: D 609 VAL cc_start: 0.7937 (t) cc_final: 0.7727 (p) REVERT: F 374 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7700 (mt0) REVERT: F 405 GLU cc_start: 0.7363 (pm20) cc_final: 0.7041 (mm-30) REVERT: F 416 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7334 (tmmm) REVERT: F 461 LEU cc_start: 0.7337 (pt) cc_final: 0.7061 (mt) REVERT: F 469 GLN cc_start: 0.4475 (mm-40) cc_final: 0.3957 (mm110) REVERT: F 555 CYS cc_start: 0.5676 (OUTLIER) cc_final: 0.5340 (p) REVERT: F 596 ASN cc_start: 0.5869 (m-40) cc_final: 0.5383 (t0) REVERT: F 604 THR cc_start: 0.5975 (p) cc_final: 0.5770 (t) REVERT: F 677 LYS cc_start: 0.7268 (tptp) cc_final: 0.7028 (ttmm) REVERT: F 684 MET cc_start: 0.4934 (tpt) cc_final: 0.4516 (tpp) outliers start: 34 outliers final: 19 residues processed: 274 average time/residue: 1.4691 time to fit residues: 438.9653 Evaluate side-chains 261 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 233 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 680 HIS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 374 GLN Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain F residue 416 LYS Chi-restraints excluded: chain F residue 436 TYR Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 571 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 0.0040 chunk 154 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 158 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 135 optimal weight: 10.0000 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 593 ASN ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 HIS E 358 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.159935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.117754 restraints weight = 17003.338| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.80 r_work: 0.3039 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 1.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16236 Z= 0.181 Angle : 0.568 11.609 21981 Z= 0.296 Chirality : 0.042 0.162 2485 Planarity : 0.004 0.061 2761 Dihedral : 9.484 138.093 2261 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.15 % Favored : 95.43 % Rotamer: Outliers : 1.77 % Allowed : 25.90 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % 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: -0.03 (0.19), residues: 1927 helix: 0.77 (0.19), residues: 729 sheet: 0.07 (0.38), residues: 229 loop : -0.60 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 675 HIS 0.006 0.001 HIS B 597 PHE 0.014 0.001 PHE F 427 TYR 0.020 0.001 TYR F 670 ARG 0.009 0.000 ARG D 663 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7402.29 seconds wall clock time: 129 minutes 48.10 seconds (7788.10 seconds total)