Starting phenix.real_space_refine (version: dev) on Fri May 13 00:37:33 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ekm_31170/05_2022/7ekm_31170.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ekm_31170/05_2022/7ekm_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_31170/05_2022/7ekm_31170.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ekm_31170/05_2022/7ekm_31170.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ekm_31170/05_2022/7ekm_31170.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ekm_31170/05_2022/7ekm_31170.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4597/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: 5.67, per 1000 atoms: 0.62 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: 3.26 Conformation dependent library (CDL) restraints added in 1.4 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: 0.61 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: 2.50 Time building geometry restraints manager: 3.57 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 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. 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: 1.170 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: 3.730 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.070 Process input model: 26.820 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 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 : 6.11 Ramachandran Plot: Outliers : 0.69 % Allowed : 6.41 % Favored : 92.89 % Rotamer Outliers : 4.77 % 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 *********************** 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 : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 6 residues processed: 179 average time/residue: 0.2314 time to fit residues: 55.4408 Evaluate side-chains 86 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 0.992 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0872 time to fit residues: 2.4990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0870 chunk 48 optimal weight: 7.9990 chunk 30 optimal weight: 0.0870 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: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 ASN A 563 ASN A 607 GLN A 665 HIS B 445 GLN B 563 ASN B 596 HIS B 607 GLN B 665 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 9298 Z= 0.168 Angle : 0.641 9.487 12612 Z= 0.342 Chirality : 0.042 0.169 1466 Planarity : 0.004 0.040 1590 Dihedral : 6.219 24.088 1280 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.16 % Favored : 95.58 % Rotamer Outliers : 2.18 % 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: -4.02 (0.22), residues: 1154 helix: -3.24 (0.16), residues: 668 sheet: 0.21 (0.57), residues: 82 loop : -1.85 (0.28), residues: 404 *********************** 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 116 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 114 average time/residue: 0.1728 time to fit residues: 29.8205 Evaluate side-chains 91 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 1.006 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0863 time to fit residues: 3.2086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 93 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 chunk 35 optimal weight: 0.0570 chunk 84 optimal weight: 0.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 ASN A 596 HIS A 652 GLN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 9298 Z= 0.146 Angle : 0.571 9.890 12612 Z= 0.303 Chirality : 0.041 0.203 1466 Planarity : 0.003 0.033 1590 Dihedral : 5.472 20.009 1280 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.77 % Favored : 94.97 % Rotamer Outliers : 1.45 % 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: -3.33 (0.23), residues: 1154 helix: -2.75 (0.18), residues: 644 sheet: 0.73 (0.55), residues: 82 loop : -1.60 (0.28), residues: 428 *********************** 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 106 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 1.006 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 102 average time/residue: 0.1674 time to fit residues: 26.4215 Evaluate side-chains 84 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 1.027 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0812 time to fit residues: 2.2452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 20.0000 chunk 79 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 112 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 501 GLN ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 ASN A 607 GLN A 617 GLN B 316 GLN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 ASN B 596 HIS B 683 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 9298 Z= 0.322 Angle : 0.680 10.712 12612 Z= 0.363 Chirality : 0.046 0.265 1466 Planarity : 0.005 0.077 1590 Dihedral : 5.760 28.554 1280 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.15 % Favored : 93.50 % Rotamer Outliers : 2.49 % 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: -3.23 (0.23), residues: 1154 helix: -2.59 (0.18), residues: 648 sheet: 0.98 (0.58), residues: 84 loop : -1.76 (0.28), residues: 422 *********************** 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 126 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 102 time to evaluate : 1.022 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 8 residues processed: 117 average time/residue: 0.1998 time to fit residues: 33.6683 Evaluate side-chains 92 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.918 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0973 time to fit residues: 2.8396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 1 optimal weight: 0.0980 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.0970 chunk 95 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN B 683 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 9298 Z= 0.129 Angle : 0.553 10.246 12612 Z= 0.287 Chirality : 0.040 0.169 1466 Planarity : 0.003 0.057 1590 Dihedral : 5.068 20.600 1280 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.16 % Favored : 95.58 % Rotamer Outliers : 1.14 % 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: -2.74 (0.23), residues: 1154 helix: -2.18 (0.19), residues: 640 sheet: 0.99 (0.57), residues: 84 loop : -1.53 (0.28), residues: 430 *********************** 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 105 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 1.069 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 102 average time/residue: 0.1919 time to fit residues: 29.0000 Evaluate side-chains 88 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 1.068 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1555 time to fit residues: 2.4445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 112 optimal weight: 0.3980 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 9298 Z= 0.232 Angle : 0.591 10.291 12612 Z= 0.311 Chirality : 0.042 0.160 1466 Planarity : 0.004 0.059 1590 Dihedral : 5.197 23.996 1280 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.11 % Favored : 94.63 % Rotamer Outliers : 1.04 % 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: -2.65 (0.24), residues: 1154 helix: -2.04 (0.20), residues: 648 sheet: 0.96 (0.56), residues: 84 loop : -1.59 (0.28), residues: 422 *********************** 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 98 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 1.036 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 94 average time/residue: 0.1674 time to fit residues: 24.1436 Evaluate side-chains 87 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 0.995 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0817 time to fit residues: 1.8881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 10.0000 chunk 63 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 20.0000 chunk 62 optimal weight: 0.5980 chunk 111 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 44 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4990 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= 0.128 Angle : 0.539 10.132 12612 Z= 0.279 Chirality : 0.040 0.162 1466 Planarity : 0.003 0.041 1590 Dihedral : 4.816 20.214 1280 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.16 % Favored : 95.58 % Rotamer Outliers : 0.31 % 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: -2.41 (0.24), residues: 1154 helix: -1.79 (0.20), residues: 650 sheet: 1.05 (0.56), residues: 84 loop : -1.57 (0.28), residues: 420 *********************** 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 85 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 1.050 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 83 average time/residue: 0.1832 time to fit residues: 23.2979 Evaluate side-chains 78 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.054 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 chunk 55 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 719 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: 0.7922 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 9298 Z= 0.210 Angle : 0.589 13.120 12612 Z= 0.299 Chirality : 0.042 0.157 1466 Planarity : 0.003 0.039 1590 Dihedral : 4.949 23.396 1280 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.20 % Favored : 94.71 % Rotamer Outliers : 0.73 % 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: -2.38 (0.24), residues: 1154 helix: -1.78 (0.20), residues: 652 sheet: 1.01 (0.57), residues: 84 loop : -1.53 (0.29), residues: 418 *********************** 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 91 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 1.050 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 86 average time/residue: 0.1888 time to fit residues: 24.2331 Evaluate side-chains 81 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 1.041 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0936 time to fit residues: 1.9594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 10.0000 chunk 62 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 98 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 683 ASN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 761 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.5448 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= 0.156 Angle : 0.571 14.176 12612 Z= 0.283 Chirality : 0.041 0.158 1466 Planarity : 0.003 0.037 1590 Dihedral : 4.761 21.493 1280 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.68 % Favored : 95.23 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.24 (0.24), residues: 1154 helix: -1.64 (0.20), residues: 654 sheet: 1.00 (0.57), residues: 84 loop : -1.49 (0.29), residues: 416 *********************** 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 84 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 1.017 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 80 average time/residue: 0.1804 time to fit residues: 22.1608 Evaluate side-chains 76 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 1.116 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1190 time to fit residues: 1.9713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 56 optimal weight: 30.0000 chunk 73 optimal weight: 0.0050 chunk 98 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- 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** A 652 GLN A 656 GLN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.5690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 9298 Z= 0.205 Angle : 0.585 14.445 12612 Z= 0.295 Chirality : 0.042 0.167 1466 Planarity : 0.003 0.036 1590 Dihedral : 4.861 25.076 1280 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.46 % Favored : 94.45 % Rotamer Outliers : 0.52 % 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: -2.16 (0.24), residues: 1154 helix: -1.57 (0.20), residues: 654 sheet: 0.93 (0.54), residues: 82 loop : -1.41 (0.29), residues: 418 ********************** 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 80 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 1.022 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 76 average time/residue: 0.1851 time to fit residues: 21.5523 Evaluate side-chains 77 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 1.036 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0921 time to fit residues: 2.0810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 0.4980 chunk 92 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 11 optimal weight: 0.4980 chunk 16 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** B 733 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.212426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.157791 restraints weight = 10075.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.152847 restraints weight = 15226.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.154873 restraints weight = 13400.406| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.5808 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= 0.121 Angle : 0.556 14.204 12612 Z= 0.274 Chirality : 0.040 0.162 1466 Planarity : 0.003 0.035 1590 Dihedral : 4.603 27.660 1280 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.42 % Favored : 95.49 % Rotamer Outliers : 0.10 % 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: -1.99 (0.24), residues: 1154 helix: -1.41 (0.21), residues: 656 sheet: 0.95 (0.54), residues: 82 loop : -1.38 (0.29), residues: 416 =============================================================================== Job complete usr+sys time: 1596.84 seconds wall clock time: 29 minutes 53.98 seconds (1793.98 seconds total)