Starting phenix.real_space_refine on Tue Mar 19 14:01:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6on2_20133/03_2024/6on2_20133_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6on2_20133/03_2024/6on2_20133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6on2_20133/03_2024/6on2_20133.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6on2_20133/03_2024/6on2_20133.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6on2_20133/03_2024/6on2_20133_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6on2_20133/03_2024/6on2_20133_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.014 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 16 5.49 5 Mg 5 5.21 5 S 138 5.16 5 C 15268 2.51 5 N 4307 2.21 5 O 4616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 433": "NH1" <-> "NH2" Residue "A ARG 648": "NH1" <-> "NH2" Residue "B ARG 396": "NH1" <-> "NH2" Residue "B PHE 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 274": "OE1" <-> "OE2" Residue "E ARG 433": "NH1" <-> "NH2" Residue "E ARG 542": "NH1" <-> "NH2" Residue "F TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24350 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4041 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 24, 'TRANS': 498} Chain: "B" Number of atoms: 4052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4052 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 24, 'TRANS': 499} Chain: "C" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4041 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 24, 'TRANS': 498} Chain: "D" Number of atoms: 4001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 4001 Classifications: {'peptide': 518} Link IDs: {'PTRANS': 24, 'TRANS': 493} Chain breaks: 1 Chain: "E" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4041 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 24, 'TRANS': 498} Chain: "F" Number of atoms: 3955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3955 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 24, 'TRANS': 487} Chain breaks: 1 Chain: "G" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 36 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 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, 'ATP': 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, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.37, per 1000 atoms: 0.47 Number of scatterers: 24350 At special positions: 0 Unit cell: (131.1, 136.85, 129.95, 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 138 16.00 P 16 15.00 Mg 5 11.99 O 4616 8.00 N 4307 7.00 C 15268 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: 9.66 Conformation dependent library (CDL) restraints added in 4.8 seconds 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5786 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 133 helices and 26 sheets defined 40.2% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.13 Creating SS restraints... Processing helix chain 'A' and resid 255 through 261 Processing helix chain 'A' and resid 265 through 280 removed outlier: 5.727A pdb=" N MET A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 299 Processing helix chain 'A' and resid 314 through 322 removed outlier: 3.797A pdb=" N THR A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 340 Processing helix chain 'A' and resid 366 through 372 Processing helix chain 'A' and resid 388 through 392 removed outlier: 3.969A pdb=" N ARG A 392 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 413 Processing helix chain 'A' and resid 436 through 443 Processing helix chain 'A' and resid 479 through 484 removed outlier: 3.770A pdb=" N ASP A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ARG A 484 " --> pdb=" O PRO A 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 479 through 484' Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 506 through 513 Processing helix chain 'A' and resid 525 through 534 Processing helix chain 'A' and resid 542 through 560 Processing helix chain 'A' and resid 632 through 646 Processing helix chain 'A' and resid 658 through 660 No H-bonds generated for 'chain 'A' and resid 658 through 660' Processing helix chain 'A' and resid 682 through 693 removed outlier: 3.552A pdb=" N THR A 686 " --> pdb=" O ILE A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 728 Processing helix chain 'A' and resid 738 through 746 removed outlier: 5.057A pdb=" N ARG A 742 " --> pdb=" O ASP A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 754 Processing helix chain 'A' and resid 763 through 770 Processing helix chain 'B' and resid 255 through 260 Processing helix chain 'B' and resid 265 through 280 removed outlier: 4.122A pdb=" N MET B 280 " --> pdb=" O GLN B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 298 Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 328 through 343 Processing helix chain 'B' and resid 364 through 372 removed outlier: 3.647A pdb=" N GLN B 367 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE B 369 " --> pdb=" O GLY B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 404 through 413 Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 439 through 441 No H-bonds generated for 'chain 'B' and resid 439 through 441' Processing helix chain 'B' and resid 449 through 451 No H-bonds generated for 'chain 'B' and resid 449 through 451' Processing helix chain 'B' and resid 479 through 482 No H-bonds generated for 'chain 'B' and resid 479 through 482' Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'B' and resid 518 through 520 No H-bonds generated for 'chain 'B' and resid 518 through 520' Processing helix chain 'B' and resid 525 through 534 Processing helix chain 'B' and resid 542 through 562 Processing helix chain 'B' and resid 575 through 579 Processing helix chain 'B' and resid 632 through 647 Processing helix chain 'B' and resid 658 through 661 No H-bonds generated for 'chain 'B' and resid 658 through 661' Processing helix chain 'B' and resid 681 through 689 Processing helix chain 'B' and resid 719 through 728 Processing helix chain 'B' and resid 738 through 746 removed outlier: 4.173A pdb=" N ARG B 742 " --> pdb=" O ASP B 739 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLU B 745 " --> pdb=" O ARG B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 754 Processing helix chain 'B' and resid 763 through 769 Processing helix chain 'C' and resid 255 through 260 Processing helix chain 'C' and resid 265 through 280 removed outlier: 4.255A pdb=" N MET C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 300 Processing helix chain 'C' and resid 313 through 323 Processing helix chain 'C' and resid 328 through 343 Processing helix chain 'C' and resid 364 through 373 Processing helix chain 'C' and resid 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' Processing helix chain 'C' and resid 405 through 413 Processing helix chain 'C' and resid 440 through 443 No H-bonds generated for 'chain 'C' and resid 440 through 443' Processing helix chain 'C' and resid 479 through 484 Processing helix chain 'C' and resid 495 through 504 Processing helix chain 'C' and resid 506 through 512 Processing helix chain 'C' and resid 525 through 534 Processing helix chain 'C' and resid 542 through 560 Processing helix chain 'C' and resid 632 through 648 Processing helix chain 'C' and resid 658 through 661 No H-bonds generated for 'chain 'C' and resid 658 through 661' Processing helix chain 'C' and resid 678 through 693 removed outlier: 5.091A pdb=" N ILE C 682 " --> pdb=" O SER C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 729 Processing helix chain 'C' and resid 738 through 746 removed outlier: 4.804A pdb=" N ARG C 742 " --> pdb=" O ASP C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 754 Processing helix chain 'C' and resid 763 through 770 Processing helix chain 'D' and resid 255 through 259 Processing helix chain 'D' and resid 265 through 279 Processing helix chain 'D' and resid 287 through 298 Processing helix chain 'D' and resid 314 through 323 Processing helix chain 'D' and resid 328 through 340 Processing helix chain 'D' and resid 363 through 373 Processing helix chain 'D' and resid 388 through 390 No H-bonds generated for 'chain 'D' and resid 388 through 390' Processing helix chain 'D' and resid 406 through 413 Processing helix chain 'D' and resid 425 through 427 No H-bonds generated for 'chain 'D' and resid 425 through 427' Processing helix chain 'D' and resid 436 through 443 removed outlier: 3.733A pdb=" N LEU D 441 " --> pdb=" O ALA D 437 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLU D 442 " --> pdb=" O SER D 438 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL D 443 " --> pdb=" O ALA D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 483 Processing helix chain 'D' and resid 495 through 504 Processing helix chain 'D' and resid 506 through 511 Processing helix chain 'D' and resid 525 through 534 Processing helix chain 'D' and resid 542 through 561 Processing helix chain 'D' and resid 632 through 647 Processing helix chain 'D' and resid 649 through 652 No H-bonds generated for 'chain 'D' and resid 649 through 652' Processing helix chain 'D' and resid 658 through 661 No H-bonds generated for 'chain 'D' and resid 658 through 661' Processing helix chain 'D' and resid 678 through 693 removed outlier: 5.225A pdb=" N ILE D 682 " --> pdb=" O SER D 679 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N CYS D 691 " --> pdb=" O LEU D 688 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR D 693 " --> pdb=" O SER D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 719 through 727 Processing helix chain 'D' and resid 738 through 746 removed outlier: 3.906A pdb=" N LYS D 741 " --> pdb=" O ASP D 738 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ARG D 742 " --> pdb=" O ASP D 739 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU D 745 " --> pdb=" O ARG D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 754 Processing helix chain 'D' and resid 763 through 770 Processing helix chain 'E' and resid 255 through 261 removed outlier: 4.160A pdb=" N GLU E 259 " --> pdb=" O LYS E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 280 Processing helix chain 'E' and resid 286 through 298 Processing helix chain 'E' and resid 314 through 320 Processing helix chain 'E' and resid 328 through 341 Processing helix chain 'E' and resid 362 through 373 Processing helix chain 'E' and resid 405 through 413 Processing helix chain 'E' and resid 436 through 442 Processing helix chain 'E' and resid 479 through 484 removed outlier: 4.587A pdb=" N ASP E 483 " --> pdb=" O ALA E 479 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ARG E 484 " --> pdb=" O PRO E 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 479 through 484' Processing helix chain 'E' and resid 495 through 504 Processing helix chain 'E' and resid 508 through 511 No H-bonds generated for 'chain 'E' and resid 508 through 511' Processing helix chain 'E' and resid 525 through 534 Processing helix chain 'E' and resid 542 through 562 Processing helix chain 'E' and resid 575 through 578 No H-bonds generated for 'chain 'E' and resid 575 through 578' Processing helix chain 'E' and resid 632 through 647 Processing helix chain 'E' and resid 656 through 661 removed outlier: 4.491A pdb=" N TYR E 659 " --> pdb=" O PRO E 656 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS E 661 " --> pdb=" O PHE E 658 " (cutoff:3.500A) Processing helix chain 'E' and resid 678 through 693 removed outlier: 5.649A pdb=" N ILE E 682 " --> pdb=" O SER E 679 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N CYS E 685 " --> pdb=" O ILE E 682 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N THR E 693 " --> pdb=" O SER E 690 " (cutoff:3.500A) Processing helix chain 'E' and resid 719 through 728 Processing helix chain 'E' and resid 741 through 746 Processing helix chain 'E' and resid 749 through 754 Processing helix chain 'E' and resid 763 through 770 removed outlier: 3.519A pdb=" N ILE E 769 " --> pdb=" O ASP E 765 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 260 Processing helix chain 'F' and resid 265 through 280 removed outlier: 3.903A pdb=" N MET F 280 " --> pdb=" O GLN F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 Processing helix chain 'F' and resid 314 through 320 Processing helix chain 'F' and resid 328 through 343 Processing helix chain 'F' and resid 365 through 373 Processing helix chain 'F' and resid 405 through 413 removed outlier: 3.840A pdb=" N MET F 410 " --> pdb=" O LEU F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 428 No H-bonds generated for 'chain 'F' and resid 425 through 428' Processing helix chain 'F' and resid 438 through 444 removed outlier: 4.363A pdb=" N VAL F 443 " --> pdb=" O ALA F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 484 removed outlier: 3.978A pdb=" N ASP F 483 " --> pdb=" O ALA F 479 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ARG F 484 " --> pdb=" O PRO F 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 479 through 484' Processing helix chain 'F' and resid 495 through 505 Processing helix chain 'F' and resid 507 through 514 Processing helix chain 'F' and resid 525 through 534 Processing helix chain 'F' and resid 543 through 560 Processing helix chain 'F' and resid 632 through 647 Processing helix chain 'F' and resid 656 through 661 removed outlier: 4.313A pdb=" N TYR F 659 " --> pdb=" O PRO F 656 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS F 661 " --> pdb=" O PHE F 658 " (cutoff:3.500A) Processing helix chain 'F' and resid 681 through 693 Processing helix chain 'F' and resid 719 through 729 Processing helix chain 'F' and resid 738 through 740 No H-bonds generated for 'chain 'F' and resid 738 through 740' Processing helix chain 'F' and resid 742 through 746 Processing helix chain 'F' and resid 749 through 754 Processing helix chain 'F' and resid 763 through 770 removed outlier: 3.505A pdb=" N ILE F 769 " --> pdb=" O ASP F 765 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 485 through 490 removed outlier: 6.551A pdb=" N ILE A 351 " --> pdb=" O GLU A 486 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE A 488 " --> pdb=" O ILE A 351 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N CYS A 353 " --> pdb=" O ILE A 488 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU A 490 " --> pdb=" O CYS A 353 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL A 355 " --> pdb=" O LEU A 490 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLN A 376 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N LEU A 421 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL A 378 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 521 through 523 removed outlier: 6.366A pdb=" N ILE A 568 " --> pdb=" O THR A 522 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 597 through 604 removed outlier: 6.769A pdb=" N LYS A 623 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N VAL A 666 " --> pdb=" O LYS A 623 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR A 625 " --> pdb=" O VAL A 666 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.783A pdb=" N VAL A 733 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLU A 756 " --> pdb=" O VAL A 734 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE A 736 " --> pdb=" O GLU A 756 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N HIS A 758 " --> pdb=" O ILE A 736 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 486 through 490 removed outlier: 6.540A pdb=" N PHE B 468 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU B 354 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA B 470 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N GLY B 356 " --> pdb=" O ALA B 470 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N SER B 472 " --> pdb=" O GLY B 356 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLN B 376 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU B 421 " --> pdb=" O GLN B 376 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL B 378 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ASP B 423 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N MET B 380 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 521 through 523 removed outlier: 6.469A pdb=" N ILE B 568 " --> pdb=" O THR B 522 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 597 through 603 Processing sheet with id= H, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.320A pdb=" N VAL B 733 " --> pdb=" O ALA B 702 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLU B 756 " --> pdb=" O VAL B 734 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE B 736 " --> pdb=" O GLU B 756 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N HIS B 758 " --> pdb=" O ILE B 736 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 486 through 490 removed outlier: 6.428A pdb=" N PHE C 468 " --> pdb=" O LEU C 352 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU C 354 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA C 470 " --> pdb=" O LEU C 354 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N GLY C 356 " --> pdb=" O ALA C 470 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N SER C 472 " --> pdb=" O GLY C 356 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLN C 376 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU C 421 " --> pdb=" O GLN C 376 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL C 378 " --> pdb=" O LEU C 421 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ASP C 423 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N MET C 380 " --> pdb=" O ASP C 423 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 521 through 523 removed outlier: 6.928A pdb=" N ILE C 568 " --> pdb=" O THR C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 598 through 603 Processing sheet with id= L, first strand: chain 'C' and resid 614 through 619 Processing sheet with id= M, first strand: chain 'C' and resid 733 through 737 removed outlier: 6.492A pdb=" N GLU C 756 " --> pdb=" O VAL C 734 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ILE C 736 " --> pdb=" O GLU C 756 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N HIS C 758 " --> pdb=" O ILE C 736 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'D' and resid 486 through 490 removed outlier: 6.827A pdb=" N PHE D 468 " --> pdb=" O LEU D 352 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU D 354 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA D 470 " --> pdb=" O LEU D 354 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N GLY D 356 " --> pdb=" O ALA D 470 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N SER D 472 " --> pdb=" O GLY D 356 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLN D 376 " --> pdb=" O LEU D 419 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU D 421 " --> pdb=" O GLN D 376 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL D 378 " --> pdb=" O LEU D 421 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ASP D 423 " --> pdb=" O VAL D 378 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N MET D 380 " --> pdb=" O ASP D 423 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 521 through 523 removed outlier: 6.545A pdb=" N ILE D 568 " --> pdb=" O THR D 522 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 597 through 603 Processing sheet with id= Q, first strand: chain 'D' and resid 701 through 703 removed outlier: 6.474A pdb=" N VAL D 733 " --> pdb=" O ALA D 702 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLU D 756 " --> pdb=" O VAL D 734 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE D 736 " --> pdb=" O GLU D 756 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N HIS D 758 " --> pdb=" O ILE D 736 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'E' and resid 485 through 487 removed outlier: 6.032A pdb=" N ILE E 351 " --> pdb=" O GLU E 486 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU E 352 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLN E 376 " --> pdb=" O LEU E 419 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU E 421 " --> pdb=" O GLN E 376 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL E 378 " --> pdb=" O LEU E 421 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ASP E 423 " --> pdb=" O VAL E 378 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N MET E 380 " --> pdb=" O ASP E 423 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 521 through 523 removed outlier: 6.722A pdb=" N ILE E 568 " --> pdb=" O THR E 522 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'E' and resid 598 through 604 Processing sheet with id= U, first strand: chain 'E' and resid 614 through 619 Processing sheet with id= V, first strand: chain 'E' and resid 701 through 703 removed outlier: 6.221A pdb=" N VAL E 733 " --> pdb=" O ALA E 702 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU E 756 " --> pdb=" O VAL E 734 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE E 736 " --> pdb=" O GLU E 756 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N HIS E 758 " --> pdb=" O ILE E 736 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'F' and resid 485 through 490 removed outlier: 6.862A pdb=" N ILE F 351 " --> pdb=" O GLU F 486 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE F 488 " --> pdb=" O ILE F 351 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N CYS F 353 " --> pdb=" O ILE F 488 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LEU F 490 " --> pdb=" O CYS F 353 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL F 355 " --> pdb=" O LEU F 490 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU F 352 " --> pdb=" O PHE F 468 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL F 469 " --> pdb=" O PRO F 418 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N PHE F 420 " --> pdb=" O VAL F 469 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N THR F 471 " --> pdb=" O PHE F 420 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU F 422 " --> pdb=" O THR F 471 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLN F 376 " --> pdb=" O LEU F 419 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LEU F 421 " --> pdb=" O GLN F 376 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL F 378 " --> pdb=" O LEU F 421 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N ASP F 423 " --> pdb=" O VAL F 378 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N MET F 380 " --> pdb=" O ASP F 423 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 521 through 523 removed outlier: 6.860A pdb=" N ILE F 568 " --> pdb=" O THR F 522 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'F' and resid 597 through 603 Processing sheet with id= Z, first strand: chain 'F' and resid 701 through 703 removed outlier: 6.338A pdb=" N VAL F 733 " --> pdb=" O ALA F 702 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU F 756 " --> pdb=" O VAL F 734 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ILE F 736 " --> pdb=" O GLU F 756 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N HIS F 758 " --> pdb=" O ILE F 736 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z 852 hydrogen bonds defined for protein. 2331 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.50 Time building geometry restraints manager: 10.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4769 1.33 - 1.45: 5039 1.45 - 1.57: 14621 1.57 - 1.69: 26 1.69 - 1.81: 246 Bond restraints: 24701 Sorted by residual: bond pdb=" C4 ATP B 801 " pdb=" C5 ATP B 801 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.05e+01 bond pdb=" C4 ATP C 801 " pdb=" C5 ATP C 801 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.96e+01 bond pdb=" C4 ATP D 801 " pdb=" C5 ATP D 801 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.91e+01 bond pdb=" C4 ATP A 801 " pdb=" C5 ATP A 801 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.48e+01 bond pdb=" C5 ATP B 801 " pdb=" C6 ATP B 801 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.17e+01 ... (remaining 24696 not shown) Histogram of bond angle deviations from ideal: 94.21 - 102.56: 139 102.56 - 110.91: 8721 110.91 - 119.26: 12512 119.26 - 127.61: 11830 127.61 - 135.96: 169 Bond angle restraints: 33371 Sorted by residual: angle pdb=" PB ATP C 801 " pdb=" O3B ATP C 801 " pdb=" PG ATP C 801 " ideal model delta sigma weight residual 139.87 121.87 18.00 1.00e+00 1.00e+00 3.24e+02 angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 122.25 17.62 1.00e+00 1.00e+00 3.10e+02 angle pdb=" PB ATP B 801 " pdb=" O3B ATP B 801 " pdb=" PG ATP B 801 " ideal model delta sigma weight residual 139.87 122.34 17.53 1.00e+00 1.00e+00 3.07e+02 angle pdb=" PB ATP D 801 " pdb=" O3B ATP D 801 " pdb=" PG ATP D 801 " ideal model delta sigma weight residual 139.87 122.75 17.12 1.00e+00 1.00e+00 2.93e+02 angle pdb=" PA ATP D 801 " pdb=" O3A ATP D 801 " pdb=" PB ATP D 801 " ideal model delta sigma weight residual 136.83 121.66 15.17 1.00e+00 1.00e+00 2.30e+02 ... (remaining 33366 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.70: 15056 23.70 - 47.40: 357 47.40 - 71.10: 31 71.10 - 94.80: 4 94.80 - 118.50: 1 Dihedral angle restraints: 15449 sinusoidal: 6465 harmonic: 8984 Sorted by residual: dihedral pdb=" C5' ADP E 801 " pdb=" O5' ADP E 801 " pdb=" PA ADP E 801 " pdb=" O2A ADP E 801 " ideal model delta sinusoidal sigma weight residual -60.00 -178.50 118.50 1 2.00e+01 2.50e-03 3.55e+01 dihedral pdb=" CA LEU A 422 " pdb=" C LEU A 422 " pdb=" N ASP A 423 " pdb=" CA ASP A 423 " ideal model delta harmonic sigma weight residual 180.00 -153.39 -26.61 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA VAL E 668 " pdb=" C VAL E 668 " pdb=" N PRO E 669 " pdb=" CA PRO E 669 " ideal model delta harmonic sigma weight residual -180.00 -153.99 -26.01 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 15446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2298 0.045 - 0.090: 1153 0.090 - 0.135: 330 0.135 - 0.181: 67 0.181 - 0.226: 15 Chirality restraints: 3863 Sorted by residual: chirality pdb=" CA VAL F 378 " pdb=" N VAL F 378 " pdb=" C VAL F 378 " pdb=" CB VAL F 378 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB VAL F 581 " pdb=" CA VAL F 581 " pdb=" CG1 VAL F 581 " pdb=" CG2 VAL F 581 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA PRO F 669 " pdb=" N PRO F 669 " pdb=" C PRO F 669 " pdb=" CB PRO F 669 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 3860 not shown) Planarity restraints: 4272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 689 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.30e+00 pdb=" C VAL A 689 " -0.050 2.00e-02 2.50e+03 pdb=" O VAL A 689 " 0.019 2.00e-02 2.50e+03 pdb=" N SER A 690 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 690 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.54e+00 pdb=" C SER C 690 " 0.048 2.00e-02 2.50e+03 pdb=" O SER C 690 " -0.018 2.00e-02 2.50e+03 pdb=" N CYS C 691 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 684 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.53e+00 pdb=" C MET C 684 " -0.047 2.00e-02 2.50e+03 pdb=" O MET C 684 " 0.018 2.00e-02 2.50e+03 pdb=" N CYS C 685 " 0.016 2.00e-02 2.50e+03 ... (remaining 4269 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 281 2.64 - 3.20: 21091 3.20 - 3.77: 37464 3.77 - 4.33: 54100 4.33 - 4.90: 86398 Nonbonded interactions: 199334 Sorted by model distance: nonbonded pdb=" O2G ATP B 801 " pdb="MG MG B 802 " model vdw 2.073 2.170 nonbonded pdb=" OG1 THR B 363 " pdb="MG MG B 802 " model vdw 2.076 2.170 nonbonded pdb=" OG1 THR A 363 " pdb="MG MG A 802 " model vdw 2.081 2.170 nonbonded pdb=" O3G ATP A 801 " pdb="MG MG A 802 " model vdw 2.097 2.170 nonbonded pdb=" O2G ATP D 801 " pdb="MG MG D 802 " model vdw 2.112 2.170 ... (remaining 199329 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 253 through 383 or resid 395 through 585 or resid 591 thro \ ugh 775)) selection = (chain 'B' and (resid 253 through 383 or resid 395 through 585 or resid 591 thro \ ugh 775)) selection = (chain 'C' and (resid 253 through 383 or resid 395 through 585 or resid 591 thro \ ugh 775)) selection = (chain 'D' and (resid 253 through 383 or resid 395 through 775)) selection = (chain 'E' and (resid 253 through 383 or resid 395 through 585 or resid 591 thro \ ugh 775)) selection = (chain 'F' and (resid 253 through 585 or resid 591 through 775)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.070 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: 2.030 Check model and map are aligned: 0.370 Set scattering table: 0.280 Process input model: 61.430 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.090 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:15.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 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 : 0.006 0.078 24701 Z= 0.401 Angle : 0.983 18.001 33371 Z= 0.605 Chirality : 0.057 0.226 3863 Planarity : 0.008 0.065 4272 Dihedral : 10.370 118.500 9663 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.82 % Favored : 96.14 % Rotamer: Outliers : 0.42 % Allowed : 3.05 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.12), residues: 3112 helix: -3.11 (0.10), residues: 1343 sheet: -1.47 (0.22), residues: 492 loop : -2.38 (0.14), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 603 HIS 0.011 0.002 HIS A 324 PHE 0.026 0.003 PHE D 420 TYR 0.022 0.003 TYR C 493 ARG 0.015 0.001 ARG A 710 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 613 time to evaluate : 3.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 ASP cc_start: 0.7794 (p0) cc_final: 0.7567 (p0) REVERT: A 332 ASP cc_start: 0.7265 (m-30) cc_final: 0.7001 (m-30) REVERT: A 408 GLN cc_start: 0.8613 (mt0) cc_final: 0.8287 (mt0) REVERT: B 274 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7754 (tp30) REVERT: B 472 SER cc_start: 0.8867 (p) cc_final: 0.8663 (t) REVERT: C 604 THR cc_start: 0.8401 (p) cc_final: 0.8198 (p) REVERT: C 754 ASP cc_start: 0.7890 (m-30) cc_final: 0.7656 (m-30) REVERT: D 323 ASP cc_start: 0.7524 (p0) cc_final: 0.7244 (p0) REVERT: D 371 LYS cc_start: 0.8552 (tmtp) cc_final: 0.8314 (tttm) REVERT: D 410 MET cc_start: 0.9177 (mmm) cc_final: 0.8786 (mmm) REVERT: D 669 PRO cc_start: 0.8312 (Cg_endo) cc_final: 0.8096 (Cg_exo) REVERT: E 265 LYS cc_start: 0.7351 (mmmt) cc_final: 0.7077 (mmtt) REVERT: E 304 ASN cc_start: 0.7280 (m-40) cc_final: 0.6826 (m110) REVERT: E 388 GLU cc_start: 0.7707 (tt0) cc_final: 0.6793 (pm20) REVERT: E 406 LEU cc_start: 0.7517 (tm) cc_final: 0.7222 (tt) REVERT: E 440 LEU cc_start: 0.7660 (mt) cc_final: 0.7457 (mt) REVERT: E 453 ASN cc_start: 0.7668 (p0) cc_final: 0.7034 (p0) REVERT: E 538 GLU cc_start: 0.5868 (tt0) cc_final: 0.5620 (tt0) REVERT: F 402 MET cc_start: 0.5628 (mmm) cc_final: 0.5189 (ttm) REVERT: F 410 MET cc_start: 0.8701 (mmm) cc_final: 0.8468 (mmt) REVERT: F 487 VAL cc_start: 0.8410 (t) cc_final: 0.8156 (t) outliers start: 11 outliers final: 3 residues processed: 621 average time/residue: 1.6927 time to fit residues: 1174.7156 Evaluate side-chains 437 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 434 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain F residue 274 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 9.9990 chunk 234 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 242 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 147 optimal weight: 0.9990 chunk 180 optimal weight: 5.9990 chunk 281 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN A 324 HIS A 341 GLN A 367 GLN A 394 HIS A 448 GLN A 476 ASN A 500 ASN A 510 GLN B 449 ASN B 455 HIS B 500 ASN B 505 HIS B 558 ASN B 571 ASN C 453 ASN C 476 ASN D 304 ASN D 408 GLN D 455 HIS D 505 HIS D 773 HIS E 304 ASN E 408 GLN ** E 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 574 ASN E 655 ASN F 324 HIS F 500 ASN F 558 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 24701 Z= 0.309 Angle : 0.627 12.593 33371 Z= 0.320 Chirality : 0.047 0.214 3863 Planarity : 0.006 0.047 4272 Dihedral : 8.251 94.671 3551 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.28 % Allowed : 13.03 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.13), residues: 3112 helix: -1.33 (0.12), residues: 1418 sheet: -0.96 (0.23), residues: 472 loop : -1.88 (0.15), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 603 HIS 0.005 0.002 HIS A 505 PHE 0.014 0.002 PHE B 468 TYR 0.020 0.002 TYR A 493 ARG 0.007 0.001 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 448 time to evaluate : 2.891 Fit side-chains REVERT: A 265 LYS cc_start: 0.8504 (ptmm) cc_final: 0.8257 (tptt) REVERT: A 432 MET cc_start: 0.6248 (mpm) cc_final: 0.5819 (ttp) REVERT: A 592 GLU cc_start: 0.7497 (tt0) cc_final: 0.7278 (tt0) REVERT: A 660 GLU cc_start: 0.6924 (mp0) cc_final: 0.6451 (mp0) REVERT: B 346 LYS cc_start: 0.8318 (tptp) cc_final: 0.8013 (tptt) REVERT: B 444 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8852 (pp) REVERT: C 583 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8227 (mptp) REVERT: C 604 THR cc_start: 0.8674 (p) cc_final: 0.8288 (t) REVERT: C 769 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8504 (mt) REVERT: D 271 THR cc_start: 0.8815 (t) cc_final: 0.8575 (t) REVERT: D 410 MET cc_start: 0.9131 (mmm) cc_final: 0.8807 (mmm) REVERT: E 265 LYS cc_start: 0.7316 (mmmt) cc_final: 0.6814 (tptp) REVERT: E 304 ASN cc_start: 0.7340 (m110) cc_final: 0.6888 (m110) REVERT: E 388 GLU cc_start: 0.7684 (tt0) cc_final: 0.6750 (pm20) REVERT: E 441 LEU cc_start: 0.7627 (tm) cc_final: 0.7287 (tp) REVERT: E 453 ASN cc_start: 0.7628 (p0) cc_final: 0.7062 (p0) REVERT: E 460 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7615 (t0) REVERT: E 651 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7338 (pttt) REVERT: F 263 MET cc_start: 0.7171 (mtp) cc_final: 0.6410 (ttm) REVERT: F 280 MET cc_start: 0.5446 (mpp) cc_final: 0.4902 (tpt) REVERT: F 402 MET cc_start: 0.5701 (mmm) cc_final: 0.5274 (ttp) REVERT: F 405 LYS cc_start: 0.5957 (OUTLIER) cc_final: 0.3987 (pttm) REVERT: F 513 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7524 (ptp-110) outliers start: 86 outliers final: 24 residues processed: 495 average time/residue: 1.5100 time to fit residues: 845.6283 Evaluate side-chains 436 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 405 time to evaluate : 3.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 765 ASP Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 537 ARG Chi-restraints excluded: chain C residue 583 LYS Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 651 LYS Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 764 ASP Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 388 GLU Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 512 GLU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 634 MET Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain E residue 460 ASP Chi-restraints excluded: chain E residue 651 LYS Chi-restraints excluded: chain F residue 405 LYS Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 513 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 234 optimal weight: 7.9990 chunk 191 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 282 optimal weight: 9.9990 chunk 304 optimal weight: 9.9990 chunk 251 optimal weight: 5.9990 chunk 279 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 226 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN A 367 GLN A 476 ASN B 449 ASN D 473 ASN E 408 GLN E 424 GLN ** E 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 24701 Z= 0.349 Angle : 0.625 9.486 33371 Z= 0.316 Chirality : 0.047 0.214 3863 Planarity : 0.005 0.057 4272 Dihedral : 8.152 91.895 3548 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.89 % Allowed : 14.18 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.14), residues: 3112 helix: -0.55 (0.13), residues: 1419 sheet: -0.65 (0.24), residues: 468 loop : -1.62 (0.16), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 603 HIS 0.007 0.002 HIS A 665 PHE 0.022 0.002 PHE A 420 TYR 0.018 0.002 TYR C 398 ARG 0.006 0.001 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 430 time to evaluate : 2.766 Fit side-chains revert: symmetry clash REVERT: A 265 LYS cc_start: 0.8473 (ptmm) cc_final: 0.8172 (tptt) REVERT: A 306 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7977 (ttp80) REVERT: A 421 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8124 (tm) REVERT: A 432 MET cc_start: 0.6276 (mpm) cc_final: 0.5795 (ttp) REVERT: A 592 GLU cc_start: 0.7554 (tt0) cc_final: 0.7311 (tt0) REVERT: B 346 LYS cc_start: 0.8158 (tptp) cc_final: 0.7934 (tptt) REVERT: B 444 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8917 (pp) REVERT: B 684 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7231 (mtt) REVERT: C 270 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8236 (tptp) REVERT: C 276 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7563 (tp40) REVERT: C 583 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8266 (mptp) REVERT: C 604 THR cc_start: 0.8767 (p) cc_final: 0.8417 (t) REVERT: C 739 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7565 (m-30) REVERT: D 410 MET cc_start: 0.9101 (mmm) cc_final: 0.8751 (mmm) REVERT: D 465 ASP cc_start: 0.8184 (t70) cc_final: 0.7978 (t0) REVERT: E 265 LYS cc_start: 0.7132 (mmmt) cc_final: 0.6911 (tptp) REVERT: E 281 MET cc_start: 0.4497 (ptp) cc_final: 0.4249 (ptp) REVERT: E 388 GLU cc_start: 0.7656 (tt0) cc_final: 0.6817 (pm20) REVERT: E 396 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.5605 (ptm-80) REVERT: E 453 ASN cc_start: 0.7582 (p0) cc_final: 0.7011 (p0) REVERT: E 460 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7469 (t0) REVERT: E 485 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7261 (mtm) REVERT: E 651 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7207 (pttt) REVERT: F 280 MET cc_start: 0.5450 (mpp) cc_final: 0.4806 (tpt) REVERT: F 405 LYS cc_start: 0.6031 (OUTLIER) cc_final: 0.4082 (pttm) REVERT: F 513 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7523 (ptp-110) outliers start: 102 outliers final: 46 residues processed: 489 average time/residue: 1.5538 time to fit residues: 856.5478 Evaluate side-chains 460 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 400 time to evaluate : 2.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain B residue 765 ASP Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 537 ARG Chi-restraints excluded: chain C residue 583 LYS Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 651 LYS Chi-restraints excluded: chain C residue 673 THR Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 764 ASP Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 388 GLU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 512 GLU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 634 MET Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 396 ARG Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 460 ASP Chi-restraints excluded: chain E residue 485 MET Chi-restraints excluded: chain E residue 625 THR Chi-restraints excluded: chain E residue 651 LYS Chi-restraints excluded: chain F residue 405 LYS Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 513 ARG Chi-restraints excluded: chain F residue 739 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 20.0000 chunk 212 optimal weight: 9.9990 chunk 146 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 134 optimal weight: 8.9990 chunk 189 optimal weight: 9.9990 chunk 283 optimal weight: 1.9990 chunk 299 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 chunk 268 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 GLN B 449 ASN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 453 ASN D 341 GLN D 449 ASN E 304 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24701 Z= 0.234 Angle : 0.566 10.942 33371 Z= 0.283 Chirality : 0.045 0.182 3863 Planarity : 0.005 0.051 4272 Dihedral : 7.876 88.680 3548 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.28 % Allowed : 16.20 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.15), residues: 3112 helix: 0.05 (0.14), residues: 1407 sheet: -0.45 (0.24), residues: 468 loop : -1.42 (0.16), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 603 HIS 0.004 0.001 HIS A 665 PHE 0.018 0.001 PHE A 420 TYR 0.012 0.001 TYR A 294 ARG 0.006 0.000 ARG B 489 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 421 time to evaluate : 3.031 Fit side-chains revert: symmetry clash REVERT: A 291 VAL cc_start: 0.9092 (m) cc_final: 0.8876 (p) REVERT: A 392 ARG cc_start: 0.6989 (mtp180) cc_final: 0.6726 (mtp180) REVERT: A 421 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8174 (tm) REVERT: A 432 MET cc_start: 0.6274 (mpm) cc_final: 0.5808 (ttp) REVERT: A 592 GLU cc_start: 0.7537 (tt0) cc_final: 0.7308 (tt0) REVERT: A 660 GLU cc_start: 0.6691 (mp0) cc_final: 0.6095 (mp0) REVERT: B 650 ASP cc_start: 0.7906 (t70) cc_final: 0.7646 (t0) REVERT: C 276 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7583 (tp40) REVERT: C 388 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7735 (tm-30) REVERT: C 604 THR cc_start: 0.8764 (p) cc_final: 0.8415 (t) REVERT: D 266 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7782 (m-30) REVERT: D 420 PHE cc_start: 0.9122 (OUTLIER) cc_final: 0.8402 (t80) REVERT: D 576 LYS cc_start: 0.8400 (mptt) cc_final: 0.8140 (mptp) REVERT: E 281 MET cc_start: 0.4418 (ptp) cc_final: 0.4194 (ptp) REVERT: E 375 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8183 (mtp85) REVERT: E 388 GLU cc_start: 0.7477 (tt0) cc_final: 0.6705 (pm20) REVERT: E 453 ASN cc_start: 0.7799 (p0) cc_final: 0.7209 (p0) REVERT: E 588 ARG cc_start: 0.8552 (ptp-110) cc_final: 0.8215 (ptp90) REVERT: E 651 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7201 (pttt) REVERT: F 280 MET cc_start: 0.5330 (mpp) cc_final: 0.4650 (tpt) REVERT: F 405 LYS cc_start: 0.6015 (OUTLIER) cc_final: 0.4086 (pttm) REVERT: F 684 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7950 (mmt) outliers start: 86 outliers final: 42 residues processed: 468 average time/residue: 1.5925 time to fit residues: 839.2973 Evaluate side-chains 445 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 395 time to evaluate : 2.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain B residue 739 ASP Chi-restraints excluded: chain B residue 765 ASP Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 651 LYS Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 764 ASP Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 405 LYS Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 512 GLU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 634 MET Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain E residue 375 ARG Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 651 LYS Chi-restraints excluded: chain F residue 405 LYS Chi-restraints excluded: chain F residue 428 MET Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 684 MET Chi-restraints excluded: chain F residue 739 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 0.9980 chunk 170 optimal weight: 20.0000 chunk 4 optimal weight: 0.9990 chunk 223 optimal weight: 8.9990 chunk 123 optimal weight: 7.9990 chunk 255 optimal weight: 0.7980 chunk 207 optimal weight: 30.0000 chunk 0 optimal weight: 40.0000 chunk 153 optimal weight: 6.9990 chunk 268 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 ASN D 304 ASN E 304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24701 Z= 0.224 Angle : 0.557 10.573 33371 Z= 0.277 Chirality : 0.044 0.186 3863 Planarity : 0.004 0.051 4272 Dihedral : 7.703 86.146 3548 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.62 % Allowed : 16.73 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.15), residues: 3112 helix: 0.40 (0.14), residues: 1404 sheet: -0.35 (0.24), residues: 483 loop : -1.29 (0.17), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 603 HIS 0.004 0.001 HIS C 324 PHE 0.013 0.001 PHE A 420 TYR 0.012 0.001 TYR A 294 ARG 0.010 0.000 ARG F 742 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 416 time to evaluate : 3.044 Fit side-chains revert: symmetry clash REVERT: A 291 VAL cc_start: 0.9103 (m) cc_final: 0.8869 (p) REVERT: A 432 MET cc_start: 0.6256 (mpm) cc_final: 0.5798 (ttp) REVERT: A 592 GLU cc_start: 0.7575 (tt0) cc_final: 0.7297 (tt0) REVERT: A 604 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8291 (m) REVERT: A 660 GLU cc_start: 0.6806 (mp0) cc_final: 0.6301 (tt0) REVERT: B 650 ASP cc_start: 0.7934 (t70) cc_final: 0.7659 (t0) REVERT: B 684 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7164 (mtt) REVERT: C 256 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.8146 (ptp-170) REVERT: C 276 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7580 (tp40) REVERT: C 583 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8213 (mptp) REVERT: C 604 THR cc_start: 0.8762 (p) cc_final: 0.8420 (t) REVERT: C 632 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6813 (tt0) REVERT: C 769 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8307 (mp) REVERT: D 266 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7755 (m-30) REVERT: D 420 PHE cc_start: 0.9116 (OUTLIER) cc_final: 0.8408 (t80) REVERT: D 467 MET cc_start: 0.8525 (ttp) cc_final: 0.8313 (ttt) REVERT: D 594 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7066 (mmp80) REVERT: E 265 LYS cc_start: 0.7339 (mmmt) cc_final: 0.7127 (tptp) REVERT: E 281 MET cc_start: 0.4352 (ptp) cc_final: 0.4142 (ptp) REVERT: E 284 MET cc_start: 0.5235 (tpp) cc_final: 0.4996 (tpp) REVERT: E 375 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8170 (mtp85) REVERT: E 388 GLU cc_start: 0.7414 (tt0) cc_final: 0.6709 (pm20) REVERT: E 420 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.7567 (m-80) REVERT: E 423 ASP cc_start: 0.7128 (t70) cc_final: 0.6906 (t70) REVERT: E 453 ASN cc_start: 0.7812 (p0) cc_final: 0.7237 (p0) REVERT: E 651 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.7272 (ptmt) REVERT: F 280 MET cc_start: 0.5214 (mpp) cc_final: 0.4630 (tpt) REVERT: F 405 LYS cc_start: 0.5982 (OUTLIER) cc_final: 0.4125 (pttm) REVERT: F 513 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7496 (ptp-110) REVERT: F 684 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7787 (mpp) outliers start: 95 outliers final: 47 residues processed: 469 average time/residue: 1.5952 time to fit residues: 842.3825 Evaluate side-chains 465 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 402 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain B residue 739 ASP Chi-restraints excluded: chain B residue 765 ASP Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 583 LYS Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 632 GLU Chi-restraints excluded: chain C residue 651 LYS Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 764 ASP Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 405 LYS Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 512 GLU Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 634 MET Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 762 ARG Chi-restraints excluded: chain E residue 375 ARG Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 420 PHE Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 625 THR Chi-restraints excluded: chain E residue 651 LYS Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 405 LYS Chi-restraints excluded: chain F residue 428 MET Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 513 ARG Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 684 MET Chi-restraints excluded: chain F residue 739 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 9.9990 chunk 269 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 175 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 299 optimal weight: 0.0970 chunk 248 optimal weight: 7.9990 chunk 138 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN A 639 GLN B 449 ASN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 500 ASN D 304 ASN D 341 GLN E 304 ASN E 455 HIS E 639 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24701 Z= 0.144 Angle : 0.520 9.295 33371 Z= 0.257 Chirality : 0.043 0.166 3863 Planarity : 0.004 0.051 4272 Dihedral : 7.254 82.229 3548 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.86 % Allowed : 17.45 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.15), residues: 3112 helix: 0.84 (0.15), residues: 1381 sheet: -0.23 (0.24), residues: 494 loop : -1.06 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 603 HIS 0.003 0.001 HIS D 324 PHE 0.006 0.001 PHE D 658 TYR 0.013 0.001 TYR A 294 ARG 0.007 0.000 ARG B 489 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 421 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 ASP cc_start: 0.7663 (p0) cc_final: 0.7426 (p0) REVERT: A 291 VAL cc_start: 0.9071 (m) cc_final: 0.8864 (p) REVERT: A 425 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8489 (mm) REVERT: A 432 MET cc_start: 0.6177 (mpm) cc_final: 0.5763 (ttp) REVERT: A 435 ASP cc_start: 0.7818 (t0) cc_final: 0.7597 (t70) REVERT: A 592 GLU cc_start: 0.7513 (tt0) cc_final: 0.7226 (tt0) REVERT: B 346 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8104 (tppt) REVERT: B 650 ASP cc_start: 0.7904 (t70) cc_final: 0.7638 (t0) REVERT: C 604 THR cc_start: 0.8643 (p) cc_final: 0.8298 (t) REVERT: C 769 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8369 (mt) REVERT: D 348 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7603 (ptmm) REVERT: D 420 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.8413 (t80) REVERT: D 467 MET cc_start: 0.8530 (ttp) cc_final: 0.8283 (ttt) REVERT: D 545 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7153 (tm-30) REVERT: D 592 GLU cc_start: 0.7195 (pm20) cc_final: 0.6848 (pm20) REVERT: D 594 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7221 (mmp80) REVERT: D 679 SER cc_start: 0.8727 (OUTLIER) cc_final: 0.8499 (m) REVERT: E 281 MET cc_start: 0.4104 (ptp) cc_final: 0.3826 (ptp) REVERT: E 420 PHE cc_start: 0.8610 (OUTLIER) cc_final: 0.7618 (m-80) REVERT: E 423 ASP cc_start: 0.7157 (t70) cc_final: 0.6932 (t70) REVERT: E 453 ASN cc_start: 0.7805 (p0) cc_final: 0.7208 (p0) REVERT: E 476 ASN cc_start: 0.8188 (m110) cc_final: 0.7806 (t0) REVERT: E 588 ARG cc_start: 0.8646 (ptp90) cc_final: 0.8337 (ptp90) REVERT: E 651 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.7143 (pttt) REVERT: F 280 MET cc_start: 0.5223 (mpp) cc_final: 0.4531 (tpt) REVERT: F 351 ILE cc_start: 0.6675 (OUTLIER) cc_final: 0.6162 (mp) REVERT: F 684 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7666 (mpp) outliers start: 75 outliers final: 36 residues processed: 463 average time/residue: 1.6310 time to fit residues: 849.0123 Evaluate side-chains 438 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 390 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain B residue 739 ASP Chi-restraints excluded: chain B residue 765 ASP Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 764 ASP Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain D residue 405 LYS Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 489 ARG Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 420 PHE Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 625 THR Chi-restraints excluded: chain E residue 651 LYS Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 428 MET Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 684 MET Chi-restraints excluded: chain F residue 739 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 170 optimal weight: 0.0980 chunk 219 optimal weight: 7.9990 chunk 169 optimal weight: 5.9990 chunk 252 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 298 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 182 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 GLN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 567 HIS D 304 ASN D 341 GLN E 304 ASN F 510 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24701 Z= 0.278 Angle : 0.591 11.418 33371 Z= 0.291 Chirality : 0.045 0.237 3863 Planarity : 0.004 0.050 4272 Dihedral : 7.504 83.327 3548 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.12 % Allowed : 17.91 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 3112 helix: 0.81 (0.15), residues: 1383 sheet: -0.13 (0.24), residues: 474 loop : -1.02 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 603 HIS 0.004 0.001 HIS C 324 PHE 0.014 0.001 PHE A 420 TYR 0.014 0.001 TYR A 294 ARG 0.006 0.001 ARG F 742 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 398 time to evaluate : 2.909 Fit side-chains revert: symmetry clash REVERT: A 291 VAL cc_start: 0.9074 (m) cc_final: 0.8863 (p) REVERT: A 392 ARG cc_start: 0.6980 (mtp180) cc_final: 0.6442 (ptt90) REVERT: A 395 ARG cc_start: 0.8111 (tpp80) cc_final: 0.7705 (mpt90) REVERT: A 432 MET cc_start: 0.6263 (mpm) cc_final: 0.5752 (OUTLIER) REVERT: A 660 GLU cc_start: 0.6992 (mp0) cc_final: 0.6323 (tt0) REVERT: B 444 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8925 (pp) REVERT: B 650 ASP cc_start: 0.7891 (t70) cc_final: 0.7649 (t0) REVERT: B 684 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7145 (mtt) REVERT: C 583 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8221 (mptp) REVERT: D 266 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7753 (m-30) REVERT: D 348 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7657 (ptmm) REVERT: D 420 PHE cc_start: 0.9133 (OUTLIER) cc_final: 0.8435 (t80) REVERT: D 467 MET cc_start: 0.8548 (ttp) cc_final: 0.8251 (ttt) REVERT: D 594 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7061 (mmp80) REVERT: E 281 MET cc_start: 0.4143 (ptp) cc_final: 0.3873 (ptp) REVERT: E 284 MET cc_start: 0.5452 (tpp) cc_final: 0.5200 (tpp) REVERT: E 420 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.7568 (m-80) REVERT: E 453 ASN cc_start: 0.7750 (p0) cc_final: 0.7105 (p0) REVERT: E 476 ASN cc_start: 0.8241 (m110) cc_final: 0.7803 (t0) REVERT: E 485 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7359 (mtm) REVERT: E 651 LYS cc_start: 0.7588 (OUTLIER) cc_final: 0.7276 (pttt) REVERT: F 280 MET cc_start: 0.5176 (mpp) cc_final: 0.4504 (tpt) outliers start: 82 outliers final: 49 residues processed: 442 average time/residue: 1.5763 time to fit residues: 784.7825 Evaluate side-chains 445 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 387 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain B residue 739 ASP Chi-restraints excluded: chain B residue 765 ASP Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 518 LYS Chi-restraints excluded: chain C residue 583 LYS Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 764 ASP Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain D residue 405 LYS Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 634 MET Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 663 ASP Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 420 PHE Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 485 MET Chi-restraints excluded: chain E residue 625 THR Chi-restraints excluded: chain E residue 639 GLN Chi-restraints excluded: chain E residue 651 LYS Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 428 MET Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 739 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 178 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 189 optimal weight: 10.0000 chunk 203 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 234 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 GLN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 ASN D 341 GLN D 455 HIS E 304 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 24701 Z= 0.307 Angle : 0.610 11.069 33371 Z= 0.303 Chirality : 0.046 0.221 3863 Planarity : 0.005 0.052 4272 Dihedral : 7.627 84.866 3548 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.20 % Allowed : 18.22 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.15), residues: 3112 helix: 0.79 (0.14), residues: 1376 sheet: -0.07 (0.24), residues: 470 loop : -0.98 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 603 HIS 0.005 0.001 HIS A 665 PHE 0.013 0.001 PHE A 420 TYR 0.013 0.002 TYR A 626 ARG 0.012 0.001 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 401 time to evaluate : 2.592 Fit side-chains revert: symmetry clash REVERT: A 291 VAL cc_start: 0.9040 (m) cc_final: 0.8802 (p) REVERT: A 392 ARG cc_start: 0.6976 (mtp180) cc_final: 0.6454 (ptt90) REVERT: A 395 ARG cc_start: 0.8114 (tpp80) cc_final: 0.7630 (mpt90) REVERT: A 465 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7201 (t70) REVERT: A 592 GLU cc_start: 0.7546 (tt0) cc_final: 0.7310 (tt0) REVERT: A 660 GLU cc_start: 0.6980 (mp0) cc_final: 0.6193 (tt0) REVERT: B 346 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8113 (tppt) REVERT: B 650 ASP cc_start: 0.7971 (t70) cc_final: 0.7741 (t0) REVERT: B 684 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7143 (mtt) REVERT: C 566 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7343 (mttp) REVERT: C 583 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8221 (mptp) REVERT: C 769 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8495 (mt) REVERT: D 266 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7771 (m-30) REVERT: D 348 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7688 (ptmm) REVERT: D 420 PHE cc_start: 0.9134 (OUTLIER) cc_final: 0.8448 (t80) REVERT: D 467 MET cc_start: 0.8575 (ttp) cc_final: 0.8272 (ttt) REVERT: D 594 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.6699 (mmp80) REVERT: E 281 MET cc_start: 0.4029 (ptp) cc_final: 0.3775 (ptp) REVERT: E 420 PHE cc_start: 0.8719 (OUTLIER) cc_final: 0.7695 (m-80) REVERT: E 453 ASN cc_start: 0.7773 (p0) cc_final: 0.7160 (p0) REVERT: E 476 ASN cc_start: 0.8233 (m110) cc_final: 0.7832 (t0) REVERT: E 485 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7377 (mtm) REVERT: E 537 ARG cc_start: 0.7634 (tpm170) cc_final: 0.7282 (tpp-160) REVERT: E 588 ARG cc_start: 0.8594 (ptp-110) cc_final: 0.8323 (ptp90) REVERT: E 651 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7280 (pttt) REVERT: F 280 MET cc_start: 0.5140 (mpp) cc_final: 0.4404 (tpt) REVERT: F 513 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7444 (ptp-110) outliers start: 84 outliers final: 49 residues processed: 453 average time/residue: 1.6083 time to fit residues: 821.0687 Evaluate side-chains 454 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 391 time to evaluate : 2.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain B residue 739 ASP Chi-restraints excluded: chain B residue 765 ASP Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 518 LYS Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 566 LYS Chi-restraints excluded: chain C residue 583 LYS Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 764 ASP Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 634 MET Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 663 ASP Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 420 PHE Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 485 MET Chi-restraints excluded: chain E residue 625 THR Chi-restraints excluded: chain E residue 639 GLN Chi-restraints excluded: chain E residue 651 LYS Chi-restraints excluded: chain F residue 428 MET Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 513 ARG Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 739 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 5.9990 chunk 286 optimal weight: 8.9990 chunk 261 optimal weight: 9.9990 chunk 278 optimal weight: 20.0000 chunk 167 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 chunk 218 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 251 optimal weight: 3.9990 chunk 263 optimal weight: 10.0000 chunk 277 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 GLN B 449 ASN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 ASN D 341 GLN D 455 HIS E 304 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 24701 Z= 0.402 Angle : 0.675 12.030 33371 Z= 0.334 Chirality : 0.049 0.230 3863 Planarity : 0.005 0.086 4272 Dihedral : 7.822 85.960 3548 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.05 % Allowed : 18.64 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.15), residues: 3112 helix: 0.59 (0.14), residues: 1386 sheet: -0.13 (0.25), residues: 442 loop : -1.00 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 603 HIS 0.007 0.001 HIS A 665 PHE 0.015 0.002 PHE A 420 TYR 0.016 0.002 TYR A 461 ARG 0.013 0.001 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 393 time to evaluate : 3.152 Fit side-chains revert: symmetry clash REVERT: A 291 VAL cc_start: 0.9102 (m) cc_final: 0.8886 (p) REVERT: A 395 ARG cc_start: 0.8091 (tpp80) cc_final: 0.7604 (mpt90) REVERT: A 421 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8340 (tp) REVERT: A 432 MET cc_start: 0.6091 (mpm) cc_final: 0.5839 (ttp) REVERT: A 465 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7264 (t70) REVERT: A 592 GLU cc_start: 0.7554 (tt0) cc_final: 0.7309 (tt0) REVERT: A 660 GLU cc_start: 0.7025 (mp0) cc_final: 0.6642 (tt0) REVERT: B 346 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8139 (tppt) REVERT: C 309 VAL cc_start: 0.9251 (t) cc_final: 0.9013 (m) REVERT: C 566 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7367 (mttp) REVERT: C 583 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8263 (mptp) REVERT: D 266 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7783 (m-30) REVERT: D 348 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8059 (mttp) REVERT: D 405 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7226 (mttp) REVERT: D 420 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.8337 (t80) REVERT: D 467 MET cc_start: 0.8577 (ttp) cc_final: 0.8236 (ttt) REVERT: D 594 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7817 (mmp80) REVERT: E 420 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.7687 (m-80) REVERT: E 453 ASN cc_start: 0.7684 (p0) cc_final: 0.7389 (p0) REVERT: E 476 ASN cc_start: 0.8267 (m110) cc_final: 0.7842 (t0) REVERT: E 485 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7484 (mtm) REVERT: E 537 ARG cc_start: 0.7663 (tpm170) cc_final: 0.7298 (tpp-160) REVERT: E 651 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7152 (pttt) REVERT: F 280 MET cc_start: 0.4924 (mpp) cc_final: 0.4276 (tpt) REVERT: F 475 MET cc_start: 0.7138 (mmp) cc_final: 0.6545 (mmt) REVERT: F 513 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7484 (ptp-110) outliers start: 80 outliers final: 51 residues processed: 447 average time/residue: 1.5886 time to fit residues: 798.5201 Evaluate side-chains 445 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 380 time to evaluate : 2.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain B residue 739 ASP Chi-restraints excluded: chain B residue 765 ASP Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 518 LYS Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 566 LYS Chi-restraints excluded: chain C residue 583 LYS Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 764 ASP Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 405 LYS Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 634 MET Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 663 ASP Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 420 PHE Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 485 MET Chi-restraints excluded: chain E residue 625 THR Chi-restraints excluded: chain E residue 639 GLN Chi-restraints excluded: chain E residue 651 LYS Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 428 MET Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 513 ARG Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 634 MET Chi-restraints excluded: chain F residue 739 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 4.9990 chunk 294 optimal weight: 6.9990 chunk 179 optimal weight: 8.9990 chunk 139 optimal weight: 7.9990 chunk 204 optimal weight: 5.9990 chunk 308 optimal weight: 0.5980 chunk 284 optimal weight: 1.9990 chunk 245 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 189 optimal weight: 0.7980 chunk 150 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 ASN D 341 GLN D 453 ASN D 455 HIS E 304 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 24701 Z= 0.158 Angle : 0.577 11.995 33371 Z= 0.280 Chirality : 0.043 0.243 3863 Planarity : 0.004 0.054 4272 Dihedral : 7.260 85.764 3548 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.94 % Allowed : 19.63 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 3112 helix: 1.02 (0.15), residues: 1365 sheet: 0.03 (0.24), residues: 482 loop : -0.88 (0.17), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 603 HIS 0.004 0.001 HIS D 324 PHE 0.007 0.001 PHE F 420 TYR 0.010 0.001 TYR A 626 ARG 0.014 0.000 ARG A 268 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 414 time to evaluate : 2.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 395 ARG cc_start: 0.7947 (tpp80) cc_final: 0.7557 (mpt90) REVERT: A 421 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8310 (tp) REVERT: A 432 MET cc_start: 0.6013 (mpm) cc_final: 0.5797 (ttp) REVERT: A 435 ASP cc_start: 0.7934 (t0) cc_final: 0.7728 (t0) REVERT: A 465 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7157 (t70) REVERT: B 346 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8111 (tppt) REVERT: D 266 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7705 (m-30) REVERT: D 348 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7623 (ptmm) REVERT: D 420 PHE cc_start: 0.9095 (OUTLIER) cc_final: 0.8468 (t80) REVERT: D 467 MET cc_start: 0.8586 (ttp) cc_final: 0.8275 (ttt) REVERT: D 545 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7164 (tm-30) REVERT: D 594 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.6930 (mmp80) REVERT: E 281 MET cc_start: 0.3937 (ptp) cc_final: 0.3589 (ptp) REVERT: E 420 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.7710 (m-80) REVERT: E 453 ASN cc_start: 0.7779 (p0) cc_final: 0.7162 (p0) REVERT: E 476 ASN cc_start: 0.8175 (m110) cc_final: 0.7949 (t0) REVERT: E 537 ARG cc_start: 0.7563 (tpm170) cc_final: 0.7234 (tpp-160) REVERT: E 651 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.7300 (ptmt) REVERT: F 280 MET cc_start: 0.4958 (mpp) cc_final: 0.4413 (tpt) REVERT: F 745 GLU cc_start: 0.6866 (mt-10) cc_final: 0.6574 (mt-10) outliers start: 51 outliers final: 26 residues processed: 441 average time/residue: 1.6144 time to fit residues: 806.1013 Evaluate side-chains 428 residues out of total 2624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 392 time to evaluate : 2.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 765 ASP Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 764 ASP Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 663 ASP Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 420 PHE Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 651 LYS Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 634 MET Chi-restraints excluded: chain F residue 739 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 6.9990 chunk 261 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 226 optimal weight: 0.2980 chunk 36 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 246 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 252 optimal weight: 6.9990 chunk 31 optimal weight: 0.0000 chunk 45 optimal weight: 8.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 GLN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 ASN D 455 HIS E 304 ASN F 510 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.110914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.094211 restraints weight = 38337.320| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.61 r_work: 0.3060 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24701 Z= 0.165 Angle : 0.575 10.776 33371 Z= 0.280 Chirality : 0.044 0.259 3863 Planarity : 0.004 0.050 4272 Dihedral : 7.067 89.078 3548 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.56 % Allowed : 20.43 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.15), residues: 3112 helix: 1.13 (0.15), residues: 1367 sheet: 0.06 (0.24), residues: 497 loop : -0.81 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 603 HIS 0.003 0.001 HIS E 758 PHE 0.010 0.001 PHE F 420 TYR 0.012 0.001 TYR A 626 ARG 0.013 0.000 ARG A 268 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11599.46 seconds wall clock time: 204 minutes 38.01 seconds (12278.01 seconds total)