Starting phenix.real_space_refine on Thu Mar 14 15:26:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ekm_31170/03_2024/7ekm_31170.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ekm_31170/03_2024/7ekm_31170.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ekm_31170/03_2024/7ekm_31170.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ekm_31170/03_2024/7ekm_31170.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ekm_31170/03_2024/7ekm_31170.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ekm_31170/03_2024/7ekm_31170.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 5870 2.51 5 N 1574 2.21 5 O 1646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 244": "NH1" <-> "NH2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A ARG 344": "NH1" <-> "NH2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A ARG 475": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A ARG 603": "NH1" <-> "NH2" Residue "A ARG 723": "NH1" <-> "NH2" Residue "A ARG 734": "NH1" <-> "NH2" Residue "A ARG 807": "NH1" <-> "NH2" Residue "B ARG 244": "NH1" <-> "NH2" Residue "B ARG 247": "NH1" <-> "NH2" Residue "B ARG 276": "NH1" <-> "NH2" Residue "B ARG 330": "NH1" <-> "NH2" Residue "B ARG 344": "NH1" <-> "NH2" Residue "B ARG 359": "NH1" <-> "NH2" Residue "B ARG 475": "NH1" <-> "NH2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B ARG 603": "NH1" <-> "NH2" Residue "B ARG 723": "NH1" <-> "NH2" Residue "B ARG 734": "NH1" <-> "NH2" Residue "B ARG 807": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9124 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4562 Classifications: {'peptide': 581} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 568} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 4562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4562 Classifications: {'peptide': 581} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 568} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 Time building chain proxies: 5.28, per 1000 atoms: 0.58 Number of scatterers: 9124 At special positions: 0 Unit cell: (116.1, 70.52, 137.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1646 8.00 N 1574 7.00 C 5870 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: 3.16 Conformation dependent library (CDL) restraints added in 1.8 seconds 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 4 sheets defined 49.4% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 249 through 253 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 274 through 278 removed outlier: 3.656A pdb=" N LEU A 278 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 295 Processing helix chain 'A' and resid 298 through 302 Processing helix chain 'A' and resid 306 through 316 removed outlier: 3.619A pdb=" N PHE A 311 " --> pdb=" O THR A 307 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 Processing helix chain 'A' and resid 340 through 345 removed outlier: 3.549A pdb=" N ARG A 344 " --> pdb=" O PHE A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 375 removed outlier: 3.533A pdb=" N ASP A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 390 removed outlier: 3.904A pdb=" N VAL A 380 " --> pdb=" O GLY A 376 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR A 381 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 397 Processing helix chain 'A' and resid 398 through 402 removed outlier: 3.517A pdb=" N ILE A 402 " --> pdb=" O ILE A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 433 removed outlier: 4.125A pdb=" N THR A 428 " --> pdb=" O TYR A 424 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 430 " --> pdb=" O THR A 426 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 440 removed outlier: 3.609A pdb=" N ARG A 439 " --> pdb=" O ARG A 435 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG A 440 " --> pdb=" O THR A 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 435 through 440' Processing helix chain 'A' and resid 442 through 454 removed outlier: 3.931A pdb=" N ASN A 447 " --> pdb=" O ASN A 443 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 454 " --> pdb=" O ARG A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 464 removed outlier: 3.989A pdb=" N VAL A 463 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS A 464 " --> pdb=" O PHE A 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 459 through 464' Processing helix chain 'A' and resid 482 through 486 removed outlier: 3.716A pdb=" N GLY A 485 " --> pdb=" O LYS A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 499 Processing helix chain 'A' and resid 500 through 506 removed outlier: 3.996A pdb=" N ILE A 505 " --> pdb=" O GLN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 522 Processing helix chain 'A' and resid 530 through 542 removed outlier: 3.550A pdb=" N GLY A 534 " --> pdb=" O TYR A 530 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 537 " --> pdb=" O PHE A 533 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 539 " --> pdb=" O THR A 535 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 540 " --> pdb=" O TYR A 536 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N MET A 542 " --> pdb=" O ILE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 545 No H-bonds generated for 'chain 'A' and resid 543 through 545' Processing helix chain 'A' and resid 549 through 560 removed outlier: 3.649A pdb=" N GLN A 555 " --> pdb=" O TYR A 551 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN A 557 " --> pdb=" O MET A 553 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 558 " --> pdb=" O ILE A 554 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 566 removed outlier: 3.626A pdb=" N PHE A 565 " --> pdb=" O MET A 561 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 561 through 566' Processing helix chain 'A' and resid 628 through 636 removed outlier: 3.628A pdb=" N ILE A 632 " --> pdb=" O GLY A 628 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 633 " --> pdb=" O LYS A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 663 removed outlier: 3.555A pdb=" N ARG A 663 " --> pdb=" O GLN A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 685 removed outlier: 3.546A pdb=" N ARG A 685 " --> pdb=" O ALA A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 700 removed outlier: 3.515A pdb=" N ALA A 698 " --> pdb=" O ASP A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 710 removed outlier: 3.947A pdb=" N MET A 710 " --> pdb=" O HIS A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 718 removed outlier: 3.784A pdb=" N ARG A 717 " --> pdb=" O GLU A 714 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR A 718 " --> pdb=" O GLY A 715 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 714 through 718' Processing helix chain 'A' and resid 721 through 725 removed outlier: 3.722A pdb=" N GLY A 724 " --> pdb=" O GLY A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 744 removed outlier: 3.708A pdb=" N VAL A 735 " --> pdb=" O GLU A 731 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA A 736 " --> pdb=" O LYS A 732 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR A 740 " --> pdb=" O ALA A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 770 removed outlier: 3.853A pdb=" N SER A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 813 removed outlier: 3.514A pdb=" N SER A 813 " --> pdb=" O GLU A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 827 removed outlier: 3.761A pdb=" N GLN A 825 " --> pdb=" O MET A 821 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 253 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 274 through 278 removed outlier: 3.655A pdb=" N LEU B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 295 Processing helix chain 'B' and resid 298 through 302 Processing helix chain 'B' and resid 306 through 316 removed outlier: 3.619A pdb=" N PHE B 311 " --> pdb=" O THR B 307 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU B 312 " --> pdb=" O SER B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 Processing helix chain 'B' and resid 340 through 345 removed outlier: 3.549A pdb=" N ARG B 344 " --> pdb=" O PHE B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 375 removed outlier: 3.533A pdb=" N ASP B 374 " --> pdb=" O LEU B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 390 removed outlier: 3.903A pdb=" N VAL B 380 " --> pdb=" O GLY B 376 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR B 381 " --> pdb=" O THR B 377 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY B 382 " --> pdb=" O SER B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 397 Processing helix chain 'B' and resid 398 through 402 removed outlier: 3.516A pdb=" N ILE B 402 " --> pdb=" O ILE B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 433 removed outlier: 4.123A pdb=" N THR B 428 " --> pdb=" O TYR B 424 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL B 430 " --> pdb=" O THR B 426 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 440 removed outlier: 3.609A pdb=" N ARG B 439 " --> pdb=" O ARG B 435 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG B 440 " --> pdb=" O THR B 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 435 through 440' Processing helix chain 'B' and resid 442 through 454 removed outlier: 3.931A pdb=" N ASN B 447 " --> pdb=" O ASN B 443 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG B 452 " --> pdb=" O ALA B 448 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA B 453 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL B 454 " --> pdb=" O ARG B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 464 removed outlier: 3.988A pdb=" N VAL B 463 " --> pdb=" O ASN B 459 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS B 464 " --> pdb=" O PHE B 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 459 through 464' Processing helix chain 'B' and resid 482 through 486 removed outlier: 3.716A pdb=" N GLY B 485 " --> pdb=" O LYS B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 499 Processing helix chain 'B' and resid 500 through 506 removed outlier: 3.996A pdb=" N ILE B 505 " --> pdb=" O GLN B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 522 Processing helix chain 'B' and resid 530 through 542 removed outlier: 3.551A pdb=" N GLY B 534 " --> pdb=" O TYR B 530 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 537 " --> pdb=" O PHE B 533 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE B 538 " --> pdb=" O GLY B 534 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN B 539 " --> pdb=" O THR B 535 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 540 " --> pdb=" O TYR B 536 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N MET B 542 " --> pdb=" O ILE B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 545 No H-bonds generated for 'chain 'B' and resid 543 through 545' Processing helix chain 'B' and resid 549 through 560 removed outlier: 3.649A pdb=" N GLN B 555 " --> pdb=" O TYR B 551 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN B 557 " --> pdb=" O MET B 553 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE B 558 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE B 559 " --> pdb=" O GLN B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 566 removed outlier: 3.626A pdb=" N PHE B 565 " --> pdb=" O MET B 561 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP B 566 " --> pdb=" O GLU B 562 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 561 through 566' Processing helix chain 'B' and resid 628 through 636 removed outlier: 3.628A pdb=" N ILE B 632 " --> pdb=" O GLY B 628 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU B 633 " --> pdb=" O LYS B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 663 removed outlier: 3.555A pdb=" N ARG B 663 " --> pdb=" O GLN B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 685 removed outlier: 3.546A pdb=" N ARG B 685 " --> pdb=" O ALA B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 700 removed outlier: 3.515A pdb=" N ALA B 698 " --> pdb=" O ASP B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 710 removed outlier: 3.947A pdb=" N MET B 710 " --> pdb=" O HIS B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 718 removed outlier: 3.784A pdb=" N ARG B 717 " --> pdb=" O GLU B 714 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR B 718 " --> pdb=" O GLY B 715 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 714 through 718' Processing helix chain 'B' and resid 721 through 725 removed outlier: 3.722A pdb=" N GLY B 724 " --> pdb=" O GLY B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 744 removed outlier: 3.707A pdb=" N VAL B 735 " --> pdb=" O GLU B 731 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA B 736 " --> pdb=" O LYS B 732 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR B 740 " --> pdb=" O ALA B 736 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 770 removed outlier: 3.853A pdb=" N SER B 768 " --> pdb=" O ALA B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 813 removed outlier: 3.513A pdb=" N SER B 813 " --> pdb=" O GLU B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 827 removed outlier: 3.761A pdb=" N GLN B 825 " --> pdb=" O MET B 821 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY B 827 " --> pdb=" O GLN B 823 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 606 through 613 removed outlier: 7.087A pdb=" N GLN A 607 " --> pdb=" O HIS A 596 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N HIS A 596 " --> pdb=" O GLN A 607 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N VAL A 609 " --> pdb=" O ASN A 594 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 611 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL A 595 " --> pdb=" O SER A 644 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER A 644 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 666 through 669 removed outlier: 5.924A pdb=" N LEU A 619 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR A 618 " --> pdb=" O GLN A 793 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N LEU A 795 " --> pdb=" O THR A 618 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA A 620 " --> pdb=" O LEU A 795 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ILE A 797 " --> pdb=" O ALA A 620 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL A 622 " --> pdb=" O ILE A 797 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU A 804 " --> pdb=" O VAL A 796 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 606 through 613 removed outlier: 7.087A pdb=" N GLN B 607 " --> pdb=" O HIS B 596 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N HIS B 596 " --> pdb=" O GLN B 607 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N VAL B 609 " --> pdb=" O ASN B 594 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE B 611 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL B 595 " --> pdb=" O SER B 644 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N SER B 644 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 666 through 669 removed outlier: 5.924A pdb=" N LEU B 619 " --> pdb=" O VAL B 780 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR B 618 " --> pdb=" O GLN B 793 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N LEU B 795 " --> pdb=" O THR B 618 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA B 620 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ILE B 797 " --> pdb=" O ALA B 620 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL B 622 " --> pdb=" O ILE B 797 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU B 804 " --> pdb=" O VAL B 796 " (cutoff:3.500A) 252 hydrogen bonds defined for protein. 678 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2916 1.34 - 1.45: 1288 1.45 - 1.57: 5036 1.57 - 1.69: 2 1.69 - 1.81: 56 Bond restraints: 9298 Sorted by residual: bond pdb=" CB GLU B 275 " pdb=" CG GLU B 275 " ideal model delta sigma weight residual 1.520 1.587 -0.067 3.00e-02 1.11e+03 5.01e+00 bond pdb=" CB GLU A 275 " pdb=" CG GLU A 275 " ideal model delta sigma weight residual 1.520 1.586 -0.066 3.00e-02 1.11e+03 4.91e+00 bond pdb=" CA ASN A 328 " pdb=" CB ASN A 328 " ideal model delta sigma weight residual 1.530 1.563 -0.033 1.54e-02 4.22e+03 4.61e+00 bond pdb=" CA ASN B 328 " pdb=" CB ASN B 328 " ideal model delta sigma weight residual 1.530 1.563 -0.033 1.54e-02 4.22e+03 4.61e+00 bond pdb=" CG GLU B 474 " pdb=" CD GLU B 474 " ideal model delta sigma weight residual 1.516 1.569 -0.053 2.50e-02 1.60e+03 4.41e+00 ... (remaining 9293 not shown) Histogram of bond angle deviations from ideal: 100.50 - 107.20: 200 107.20 - 113.90: 5220 113.90 - 120.59: 3977 120.59 - 127.29: 3127 127.29 - 133.99: 88 Bond angle restraints: 12612 Sorted by residual: angle pdb=" N TRP B 412 " pdb=" CA TRP B 412 " pdb=" C TRP B 412 " ideal model delta sigma weight residual 113.88 104.25 9.63 1.23e+00 6.61e-01 6.13e+01 angle pdb=" N TRP A 412 " pdb=" CA TRP A 412 " pdb=" C TRP A 412 " ideal model delta sigma weight residual 113.88 104.27 9.61 1.23e+00 6.61e-01 6.10e+01 angle pdb=" N SER B 406 " pdb=" CA SER B 406 " pdb=" C SER B 406 " ideal model delta sigma weight residual 112.68 103.73 8.95 1.33e+00 5.65e-01 4.53e+01 angle pdb=" N SER A 406 " pdb=" CA SER A 406 " pdb=" C SER A 406 " ideal model delta sigma weight residual 112.68 103.75 8.93 1.33e+00 5.65e-01 4.51e+01 angle pdb=" N ILE A 480 " pdb=" CA ILE A 480 " pdb=" C ILE A 480 " ideal model delta sigma weight residual 113.43 106.86 6.57 1.09e+00 8.42e-01 3.63e+01 ... (remaining 12607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.00: 5005 15.00 - 30.00: 312 30.00 - 45.00: 103 45.00 - 60.00: 48 60.00 - 75.00: 8 Dihedral angle restraints: 5476 sinusoidal: 2134 harmonic: 3342 Sorted by residual: dihedral pdb=" CA ASN B 328 " pdb=" C ASN B 328 " pdb=" N LEU B 329 " pdb=" CA LEU B 329 " ideal model delta harmonic sigma weight residual 180.00 151.20 28.80 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ASN A 328 " pdb=" C ASN A 328 " pdb=" N LEU A 329 " pdb=" CA LEU A 329 " ideal model delta harmonic sigma weight residual 180.00 151.22 28.78 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA GLY B 324 " pdb=" C GLY B 324 " pdb=" N PHE B 325 " pdb=" CA PHE B 325 " ideal model delta harmonic sigma weight residual -180.00 -154.69 -25.31 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 5473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1066 0.048 - 0.097: 279 0.097 - 0.145: 93 0.145 - 0.194: 16 0.194 - 0.242: 12 Chirality restraints: 1466 Sorted by residual: chirality pdb=" CA ASN A 328 " pdb=" N ASN A 328 " pdb=" C ASN A 328 " pdb=" CB ASN A 328 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ASN B 328 " pdb=" N ASN B 328 " pdb=" C ASN B 328 " pdb=" CB ASN B 328 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA VAL B 388 " pdb=" N VAL B 388 " pdb=" C VAL B 388 " pdb=" CB VAL B 388 " both_signs ideal model delta sigma weight residual False 2.44 2.21 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1463 not shown) Planarity restraints: 1590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 542 " 0.044 5.00e-02 4.00e+02 6.62e-02 7.01e+00 pdb=" N PRO B 543 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 543 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 543 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 542 " -0.044 5.00e-02 4.00e+02 6.62e-02 7.00e+00 pdb=" N PRO A 543 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 543 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 543 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 314 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C PHE A 314 " 0.041 2.00e-02 2.50e+03 pdb=" O PHE A 314 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU A 315 " -0.014 2.00e-02 2.50e+03 ... (remaining 1587 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1569 2.75 - 3.29: 7832 3.29 - 3.83: 13916 3.83 - 4.36: 17175 4.36 - 4.90: 28678 Nonbonded interactions: 69170 Sorted by model distance: nonbonded pdb=" O MET B 407 " pdb=" CD2 PHE B 408 " model vdw 2.215 3.340 nonbonded pdb=" O MET A 407 " pdb=" CD2 PHE A 408 " model vdw 2.216 3.340 nonbonded pdb=" O ASN A 683 " pdb=" CD ARG A 739 " model vdw 2.237 3.440 nonbonded pdb=" O ASN B 683 " pdb=" CD ARG B 739 " model vdw 2.237 3.440 nonbonded pdb=" OD1 ASN A 328 " pdb=" NE2 GLN B 499 " model vdw 2.318 2.520 ... (remaining 69165 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' selection = chain 'B' } 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 group one per residue 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: 0.590 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: 0.010 Extract box with map and model: 3.340 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 25.730 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 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 : 0.005 0.067 9298 Z= 0.325 Angle : 1.186 10.036 12612 Z= 0.758 Chirality : 0.054 0.242 1466 Planarity : 0.006 0.066 1590 Dihedral : 13.127 75.005 3336 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.69 % Allowed : 6.41 % Favored : 92.89 % Rotamer: Outliers : 4.77 % Allowed : 4.36 % Favored : 90.87 % 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: -4.90 (0.20), residues: 1154 helix: -3.67 (0.16), residues: 678 sheet: -0.16 (0.62), residues: 82 loop : -2.74 (0.23), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 299 HIS 0.006 0.002 HIS B 706 PHE 0.028 0.002 PHE B 409 TYR 0.029 0.002 TYR A 465 ARG 0.007 0.001 ARG B 439 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 150 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 LEU cc_start: 0.4386 (OUTLIER) cc_final: 0.4152 (mp) REVERT: A 383 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7912 (tt) REVERT: B 323 THR cc_start: 0.8864 (m) cc_final: 0.8503 (p) REVERT: B 499 GLN cc_start: 0.8679 (mm-40) cc_final: 0.7939 (mm110) REVERT: B 505 ILE cc_start: 0.8998 (tp) cc_final: 0.8760 (tp) REVERT: B 542 MET cc_start: 0.8105 (mtt) cc_final: 0.7902 (mtm) outliers start: 46 outliers final: 6 residues processed: 179 average time/residue: 0.2460 time to fit residues: 58.4479 Evaluate side-chains 89 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain B residue 532 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 30 optimal weight: 0.0050 chunk 59 optimal weight: 4.9990 chunk 46 optimal weight: 0.4980 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 55 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN A 557 ASN A 607 GLN A 665 HIS B 445 GLN ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN B 596 HIS B 607 GLN B 665 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9298 Z= 0.216 Angle : 0.665 9.629 12612 Z= 0.357 Chirality : 0.043 0.159 1466 Planarity : 0.004 0.040 1590 Dihedral : 6.772 40.915 1293 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.25 % Favored : 95.49 % Rotamer: Outliers : 2.80 % Allowed : 9.02 % Favored : 88.17 % 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: -4.01 (0.22), residues: 1154 helix: -3.25 (0.17), residues: 656 sheet: 0.25 (0.57), residues: 82 loop : -1.89 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 488 HIS 0.003 0.001 HIS B 665 PHE 0.033 0.002 PHE B 408 TYR 0.021 0.002 TYR A 541 ARG 0.005 0.000 ARG A 734 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 99 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 505 ILE cc_start: 0.8940 (tp) cc_final: 0.8652 (tp) REVERT: B 542 MET cc_start: 0.8178 (mtt) cc_final: 0.7897 (mtm) REVERT: B 558 PHE cc_start: 0.7186 (m-80) cc_final: 0.6897 (m-80) REVERT: B 710 MET cc_start: 0.3694 (tpp) cc_final: 0.2944 (mmm) REVERT: B 750 LEU cc_start: 0.7789 (mp) cc_final: 0.7525 (tt) outliers start: 27 outliers final: 12 residues processed: 121 average time/residue: 0.1654 time to fit residues: 30.3427 Evaluate side-chains 96 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 781 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 29 optimal weight: 0.0870 chunk 105 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 104 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 ASN ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN A 557 ASN A 596 HIS A 652 GLN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN B 665 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9298 Z= 0.139 Angle : 0.565 10.260 12612 Z= 0.300 Chirality : 0.041 0.213 1466 Planarity : 0.003 0.029 1590 Dihedral : 5.676 38.142 1284 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.42 % Favored : 95.32 % Rotamer: Outliers : 2.70 % Allowed : 11.62 % Favored : 85.68 % 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: -3.44 (0.23), residues: 1154 helix: -2.83 (0.18), residues: 654 sheet: 0.78 (0.55), residues: 82 loop : -1.66 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 488 HIS 0.003 0.001 HIS B 665 PHE 0.025 0.001 PHE B 408 TYR 0.015 0.001 TYR B 465 ARG 0.004 0.000 ARG A 648 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 100 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 400 ILE cc_start: 0.8833 (pt) cc_final: 0.8465 (mt) REVERT: A 792 ASP cc_start: 0.7109 (t70) cc_final: 0.6715 (m-30) REVERT: B 461 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6810 (pt0) REVERT: B 505 ILE cc_start: 0.8913 (tp) cc_final: 0.8586 (tp) REVERT: B 710 MET cc_start: 0.3515 (tpp) cc_final: 0.3048 (mmm) REVERT: B 750 LEU cc_start: 0.7959 (mp) cc_final: 0.7675 (tt) outliers start: 26 outliers final: 16 residues processed: 118 average time/residue: 0.1663 time to fit residues: 29.6183 Evaluate side-chains 100 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 83 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 781 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 11 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 105 optimal weight: 8.9990 chunk 112 optimal weight: 0.0870 chunk 55 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 overall best weight: 3.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 ASN ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN A 617 GLN B 316 GLN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 HIS B 607 GLN B 683 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 9298 Z= 0.428 Angle : 0.750 11.768 12612 Z= 0.401 Chirality : 0.049 0.200 1466 Planarity : 0.005 0.071 1590 Dihedral : 6.207 36.764 1282 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.59 % Favored : 93.07 % Rotamer: Outliers : 3.84 % Allowed : 13.28 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -3.42 (0.23), residues: 1154 helix: -2.79 (0.18), residues: 652 sheet: 0.90 (0.58), residues: 84 loop : -1.74 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 546 HIS 0.003 0.001 HIS B 808 PHE 0.022 0.003 PHE B 408 TYR 0.027 0.003 TYR A 286 ARG 0.005 0.001 ARG A 663 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 106 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8424 (mp) REVERT: B 315 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8424 (mp) REVERT: B 523 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7728 (mt0) REVERT: B 565 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.7317 (t80) REVERT: B 716 TYR cc_start: 0.2179 (OUTLIER) cc_final: 0.1527 (m-10) outliers start: 37 outliers final: 18 residues processed: 133 average time/residue: 0.1881 time to fit residues: 35.7865 Evaluate side-chains 112 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 89 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 523 GLN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 716 TYR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 809 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 83 optimal weight: 0.6980 chunk 46 optimal weight: 0.0070 chunk 95 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 ASN ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9298 Z= 0.145 Angle : 0.576 10.362 12612 Z= 0.301 Chirality : 0.041 0.168 1466 Planarity : 0.003 0.029 1590 Dihedral : 5.447 35.717 1282 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.16 % Favored : 95.58 % Rotamer: Outliers : 2.59 % Allowed : 15.56 % Favored : 81.85 % 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: -2.95 (0.23), residues: 1154 helix: -2.36 (0.19), residues: 646 sheet: 0.92 (0.57), residues: 84 loop : -1.60 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 546 HIS 0.002 0.000 HIS B 808 PHE 0.014 0.001 PHE A 676 TYR 0.022 0.001 TYR A 541 ARG 0.003 0.000 ARG A 776 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 92 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 677 ASN cc_start: 0.7781 (t0) cc_final: 0.7561 (p0) REVERT: A 792 ASP cc_start: 0.7030 (t70) cc_final: 0.6678 (m-30) REVERT: B 505 ILE cc_start: 0.8891 (tp) cc_final: 0.8542 (tp) REVERT: B 565 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.7253 (t80) outliers start: 25 outliers final: 14 residues processed: 109 average time/residue: 0.1991 time to fit residues: 31.6079 Evaluate side-chains 102 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 809 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 27 optimal weight: 0.4980 chunk 112 optimal weight: 10.0000 chunk 93 optimal weight: 0.7980 chunk 51 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 HIS B 683 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9298 Z= 0.182 Angle : 0.564 10.216 12612 Z= 0.295 Chirality : 0.041 0.161 1466 Planarity : 0.003 0.046 1590 Dihedral : 5.253 34.205 1282 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.20 % Favored : 94.54 % Rotamer: Outliers : 3.01 % Allowed : 15.25 % Favored : 81.74 % 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: -2.81 (0.23), residues: 1154 helix: -2.18 (0.19), residues: 656 sheet: 1.03 (0.57), residues: 82 loop : -1.64 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 546 HIS 0.002 0.000 HIS B 808 PHE 0.014 0.001 PHE B 408 TYR 0.017 0.001 TYR B 471 ARG 0.008 0.000 ARG B 717 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 88 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 710 MET cc_start: 0.2733 (mmm) cc_final: 0.0378 (mmt) REVERT: A 792 ASP cc_start: 0.7083 (t70) cc_final: 0.6736 (m-30) REVERT: B 505 ILE cc_start: 0.8914 (tp) cc_final: 0.8552 (tp) REVERT: B 523 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.8048 (mt0) REVERT: B 565 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7296 (t80) outliers start: 29 outliers final: 17 residues processed: 106 average time/residue: 0.1692 time to fit residues: 27.3000 Evaluate side-chains 108 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 523 GLN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 668 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.0470 chunk 63 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 62 optimal weight: 0.6980 chunk 111 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 44 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9298 Z= 0.124 Angle : 0.534 11.388 12612 Z= 0.276 Chirality : 0.040 0.162 1466 Planarity : 0.003 0.026 1590 Dihedral : 4.879 32.076 1282 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.07 % Favored : 95.75 % Rotamer: Outliers : 2.07 % Allowed : 16.91 % Favored : 81.02 % 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: -2.49 (0.24), residues: 1154 helix: -1.90 (0.20), residues: 654 sheet: 1.16 (0.57), residues: 82 loop : -1.54 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 546 HIS 0.001 0.000 HIS B 808 PHE 0.010 0.001 PHE A 408 TYR 0.019 0.001 TYR A 541 ARG 0.005 0.000 ARG B 717 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: A 710 MET cc_start: 0.2566 (mmm) cc_final: 0.0660 (mmt) REVERT: A 792 ASP cc_start: 0.7049 (t70) cc_final: 0.6748 (m-30) REVERT: B 505 ILE cc_start: 0.8842 (tp) cc_final: 0.8476 (tp) REVERT: B 565 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7321 (t80) REVERT: B 710 MET cc_start: 0.4411 (tpp) cc_final: 0.3842 (mmm) outliers start: 20 outliers final: 13 residues processed: 107 average time/residue: 0.1763 time to fit residues: 27.9930 Evaluate side-chains 100 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 809 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 7.9990 chunk 21 optimal weight: 0.0030 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9298 Z= 0.203 Angle : 0.566 9.709 12612 Z= 0.293 Chirality : 0.042 0.160 1466 Planarity : 0.003 0.025 1590 Dihedral : 5.052 32.546 1282 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.55 % Favored : 94.37 % Rotamer: Outliers : 2.18 % Allowed : 16.70 % Favored : 81.12 % 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: -2.39 (0.24), residues: 1154 helix: -1.82 (0.20), residues: 650 sheet: 1.16 (0.58), residues: 82 loop : -1.48 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 546 HIS 0.003 0.001 HIS B 706 PHE 0.012 0.001 PHE A 408 TYR 0.017 0.001 TYR B 471 ARG 0.003 0.000 ARG B 717 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8367 (mp) REVERT: A 397 ASP cc_start: 0.8414 (t0) cc_final: 0.7943 (t0) REVERT: A 710 MET cc_start: 0.2545 (mmm) cc_final: 0.0756 (mmt) REVERT: B 565 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7387 (t80) REVERT: B 680 ILE cc_start: 0.7389 (OUTLIER) cc_final: 0.7119 (mp) outliers start: 21 outliers final: 15 residues processed: 96 average time/residue: 0.1698 time to fit residues: 24.9047 Evaluate side-chains 97 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 809 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 81 optimal weight: 0.0770 chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 GLN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.5507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9298 Z= 0.157 Angle : 0.564 13.528 12612 Z= 0.283 Chirality : 0.040 0.159 1466 Planarity : 0.003 0.024 1590 Dihedral : 4.851 32.105 1282 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.25 % Favored : 95.67 % Rotamer: Outliers : 2.07 % Allowed : 17.01 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.24), residues: 1154 helix: -1.68 (0.20), residues: 648 sheet: 1.12 (0.58), residues: 82 loop : -1.50 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 412 HIS 0.003 0.000 HIS B 706 PHE 0.012 0.001 PHE B 408 TYR 0.017 0.001 TYR A 541 ARG 0.003 0.000 ARG B 717 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 710 MET cc_start: 0.2196 (mmm) cc_final: 0.0696 (mmt) REVERT: B 505 ILE cc_start: 0.8892 (tp) cc_final: 0.8495 (tp) REVERT: B 565 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.7368 (t80) REVERT: B 680 ILE cc_start: 0.7367 (OUTLIER) cc_final: 0.7164 (mp) outliers start: 20 outliers final: 15 residues processed: 95 average time/residue: 0.1774 time to fit residues: 24.9485 Evaluate side-chains 94 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 542 MET Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 809 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 106 optimal weight: 0.0170 chunk 92 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 56 optimal weight: 30.0000 chunk 73 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 28 optimal weight: 0.3980 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 GLN A 656 GLN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.5630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9298 Z= 0.126 Angle : 0.550 14.282 12612 Z= 0.275 Chirality : 0.040 0.160 1466 Planarity : 0.003 0.025 1590 Dihedral : 4.691 32.326 1282 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.85 % Favored : 95.06 % Rotamer: Outliers : 1.76 % Allowed : 17.43 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.04 (0.25), residues: 1154 helix: -1.49 (0.21), residues: 646 sheet: 1.14 (0.58), residues: 82 loop : -1.39 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 412 HIS 0.002 0.000 HIS B 706 PHE 0.014 0.001 PHE B 408 TYR 0.023 0.001 TYR A 541 ARG 0.003 0.000 ARG B 717 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 1.226 Fit side-chains revert: symmetry clash REVERT: A 397 ASP cc_start: 0.8381 (t0) cc_final: 0.7889 (t0) REVERT: A 437 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8330 (ptmt) REVERT: A 710 MET cc_start: 0.2239 (mmm) cc_final: 0.0963 (mmt) REVERT: B 505 ILE cc_start: 0.8868 (tp) cc_final: 0.8483 (tp) REVERT: B 565 PHE cc_start: 0.7901 (OUTLIER) cc_final: 0.7314 (t80) REVERT: B 614 MET cc_start: 0.6288 (ptp) cc_final: 0.6037 (pmm) outliers start: 17 outliers final: 14 residues processed: 98 average time/residue: 0.1768 time to fit residues: 26.0081 Evaluate side-chains 94 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 542 MET Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 809 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.2980 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 80 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.212384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.158412 restraints weight = 10134.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.150983 restraints weight = 14205.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.153498 restraints weight = 11788.756| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.5792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9298 Z= 0.129 Angle : 0.547 14.265 12612 Z= 0.273 Chirality : 0.040 0.181 1466 Planarity : 0.002 0.025 1590 Dihedral : 4.608 32.080 1282 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.56 % Allowed : 17.95 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.84 (0.25), residues: 1154 helix: -1.33 (0.21), residues: 646 sheet: 1.18 (0.56), residues: 80 loop : -1.28 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 546 HIS 0.002 0.000 HIS B 706 PHE 0.008 0.001 PHE A 314 TYR 0.022 0.001 TYR A 541 ARG 0.004 0.000 ARG B 717 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1731.11 seconds wall clock time: 32 minutes 2.54 seconds (1922.54 seconds total)