Starting phenix.real_space_refine on Mon Apr 8 17:58:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p07_20226/04_2024/6p07_20226_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p07_20226/04_2024/6p07_20226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p07_20226/04_2024/6p07_20226.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p07_20226/04_2024/6p07_20226.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p07_20226/04_2024/6p07_20226_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p07_20226/04_2024/6p07_20226_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.125 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 20 5.49 5 Mg 6 5.21 5 S 28 5.16 5 C 8756 2.51 5 N 2481 2.21 5 O 2781 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 621": "NH1" <-> "NH2" Residue "A ARG 720": "NH1" <-> "NH2" Residue "A ARG 735": "NH1" <-> "NH2" Residue "B ARG 513": "NH1" <-> "NH2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "C ARG 505": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 14072 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2102 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 261} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2344 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 289} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2333 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 13, 'TRANS': 287} Chain: "D" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2347 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 13, 'TRANS': 289} Chain: "E" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2347 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 13, 'TRANS': 289} Chain: "F" Number of atoms: 2244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2244 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 13, 'TRANS': 286} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 46 Chain: "G" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 136 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 59 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Conformer: "B" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" C1'AATP F 801 " occ=0.50 ... (29 atoms not shown) pdb=" PG AATP F 801 " occ=0.50 residue: pdb=" C1'BADP F 802 " occ=0.50 ... (25 atoms not shown) pdb=" PB BADP F 802 " occ=0.50 Time building chain proxies: 8.42, per 1000 atoms: 0.60 Number of scatterers: 14072 At special positions: 0 Unit cell: (101.2, 133.4, 138, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 20 15.00 Mg 6 11.99 O 2781 8.00 N 2481 7.00 C 8756 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: 5.72 Conformation dependent library (CDL) restraints added in 2.6 seconds 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3382 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 93 helices and 9 sheets defined 45.3% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'A' and resid 464 through 471 removed outlier: 4.010A pdb=" N ILE A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A 470 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'A' and resid 489 through 498 Processing helix chain 'A' and resid 529 through 540 removed outlier: 3.524A pdb=" N CYS A 540 " --> pdb=" O VAL A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 552 No H-bonds generated for 'chain 'A' and resid 549 through 552' Processing helix chain 'A' and resid 560 through 573 Processing helix chain 'A' and resid 597 through 611 Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 636 through 639 No H-bonds generated for 'chain 'A' and resid 636 through 639' Processing helix chain 'A' and resid 653 through 664 Processing helix chain 'A' and resid 673 through 682 removed outlier: 3.616A pdb=" N ARG A 677 " --> pdb=" O THR A 673 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG A 678 " --> pdb=" O GLU A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 699 Processing helix chain 'A' and resid 702 through 705 Processing helix chain 'A' and resid 709 through 712 No H-bonds generated for 'chain 'A' and resid 709 through 712' Processing helix chain 'A' and resid 724 through 732 removed outlier: 4.014A pdb=" N LYS A 732 " --> pdb=" O HIS A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 749 removed outlier: 3.776A pdb=" N SER A 745 " --> pdb=" O GLN A 741 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR A 746 " --> pdb=" O SER A 742 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU A 747 " --> pdb=" O LEU A 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 471 Processing helix chain 'B' and resid 489 through 498 Processing helix chain 'B' and resid 500 through 504 Processing helix chain 'B' and resid 530 through 538 Processing helix chain 'B' and resid 549 through 551 No H-bonds generated for 'chain 'B' and resid 549 through 551' Processing helix chain 'B' and resid 559 through 573 removed outlier: 3.644A pdb=" N LEU B 563 " --> pdb=" O ASP B 559 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL B 564 " --> pdb=" O GLY B 560 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG B 565 " --> pdb=" O GLU B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 611 removed outlier: 4.174A pdb=" N ASP B 611 " --> pdb=" O LEU B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 616 No H-bonds generated for 'chain 'B' and resid 614 through 616' Processing helix chain 'B' and resid 631 through 633 No H-bonds generated for 'chain 'B' and resid 631 through 633' Processing helix chain 'B' and resid 636 through 641 removed outlier: 3.575A pdb=" N ARG B 641 " --> pdb=" O ALA B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 667 Processing helix chain 'B' and resid 673 through 682 Processing helix chain 'B' and resid 688 through 704 Proline residue: B 702 - end of helix Processing helix chain 'B' and resid 709 through 712 No H-bonds generated for 'chain 'B' and resid 709 through 712' Processing helix chain 'B' and resid 724 through 731 Processing helix chain 'B' and resid 740 through 752 removed outlier: 3.802A pdb=" N ASP B 752 " --> pdb=" O LYS B 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 472 removed outlier: 3.812A pdb=" N GLU C 472 " --> pdb=" O LEU C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 498 Processing helix chain 'C' and resid 501 through 504 No H-bonds generated for 'chain 'C' and resid 501 through 504' Processing helix chain 'C' and resid 506 through 508 No H-bonds generated for 'chain 'C' and resid 506 through 508' Processing helix chain 'C' and resid 530 through 539 Processing helix chain 'C' and resid 560 through 573 removed outlier: 3.799A pdb=" N VAL C 564 " --> pdb=" O GLY C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 610 Processing helix chain 'C' and resid 631 through 633 No H-bonds generated for 'chain 'C' and resid 631 through 633' Processing helix chain 'C' and resid 636 through 639 No H-bonds generated for 'chain 'C' and resid 636 through 639' Processing helix chain 'C' and resid 653 through 665 Processing helix chain 'C' and resid 673 through 682 Processing helix chain 'C' and resid 688 through 704 Proline residue: C 702 - end of helix Processing helix chain 'C' and resid 724 through 731 Processing helix chain 'C' and resid 740 through 747 removed outlier: 4.283A pdb=" N ASN C 744 " --> pdb=" O PRO C 740 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N SER C 745 " --> pdb=" O GLN C 741 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR C 746 " --> pdb=" O SER C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 753 Processing helix chain 'D' and resid 463 through 472 removed outlier: 3.828A pdb=" N GLU D 472 " --> pdb=" O LEU D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 484 No H-bonds generated for 'chain 'D' and resid 482 through 484' Processing helix chain 'D' and resid 489 through 498 Processing helix chain 'D' and resid 500 through 504 Processing helix chain 'D' and resid 506 through 508 No H-bonds generated for 'chain 'D' and resid 506 through 508' Processing helix chain 'D' and resid 530 through 537 Processing helix chain 'D' and resid 560 through 573 Processing helix chain 'D' and resid 597 through 611 removed outlier: 4.277A pdb=" N ASP D 611 " --> pdb=" O LEU D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 619 No H-bonds generated for 'chain 'D' and resid 617 through 619' Processing helix chain 'D' and resid 631 through 633 No H-bonds generated for 'chain 'D' and resid 631 through 633' Processing helix chain 'D' and resid 636 through 641 Processing helix chain 'D' and resid 653 through 665 Processing helix chain 'D' and resid 673 through 682 Processing helix chain 'D' and resid 688 through 704 Proline residue: D 702 - end of helix Processing helix chain 'D' and resid 724 through 731 Processing helix chain 'D' and resid 740 through 750 Processing helix chain 'E' and resid 463 through 471 Processing helix chain 'E' and resid 489 through 498 Processing helix chain 'E' and resid 501 through 503 No H-bonds generated for 'chain 'E' and resid 501 through 503' Processing helix chain 'E' and resid 511 through 513 No H-bonds generated for 'chain 'E' and resid 511 through 513' Processing helix chain 'E' and resid 530 through 538 Processing helix chain 'E' and resid 561 through 573 Processing helix chain 'E' and resid 584 through 586 No H-bonds generated for 'chain 'E' and resid 584 through 586' Processing helix chain 'E' and resid 597 through 611 removed outlier: 3.892A pdb=" N ASP E 611 " --> pdb=" O LEU E 607 " (cutoff:3.500A) Processing helix chain 'E' and resid 617 through 619 No H-bonds generated for 'chain 'E' and resid 617 through 619' Processing helix chain 'E' and resid 631 through 633 No H-bonds generated for 'chain 'E' and resid 631 through 633' Processing helix chain 'E' and resid 637 through 640 No H-bonds generated for 'chain 'E' and resid 637 through 640' Processing helix chain 'E' and resid 653 through 663 Processing helix chain 'E' and resid 674 through 682 Processing helix chain 'E' and resid 688 through 705 Proline residue: E 702 - end of helix removed outlier: 4.588A pdb=" N GLU E 705 " --> pdb=" O GLU E 701 " (cutoff:3.500A) Processing helix chain 'E' and resid 709 through 711 No H-bonds generated for 'chain 'E' and resid 709 through 711' Processing helix chain 'E' and resid 724 through 731 Processing helix chain 'E' and resid 740 through 753 removed outlier: 4.026A pdb=" N ASN E 744 " --> pdb=" O GLN E 741 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLN E 751 " --> pdb=" O LYS E 748 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR E 753 " --> pdb=" O SER E 750 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 471 Processing helix chain 'F' and resid 482 through 484 No H-bonds generated for 'chain 'F' and resid 482 through 484' Processing helix chain 'F' and resid 489 through 498 Processing helix chain 'F' and resid 531 through 539 Processing helix chain 'F' and resid 560 through 573 Processing helix chain 'F' and resid 584 through 587 No H-bonds generated for 'chain 'F' and resid 584 through 587' Processing helix chain 'F' and resid 597 through 611 removed outlier: 3.560A pdb=" N ASP F 611 " --> pdb=" O LEU F 607 " (cutoff:3.500A) Processing helix chain 'F' and resid 636 through 641 removed outlier: 3.560A pdb=" N ARG F 641 " --> pdb=" O ALA F 637 " (cutoff:3.500A) Processing helix chain 'F' and resid 653 through 667 removed outlier: 4.272A pdb=" N LYS F 666 " --> pdb=" O ARG F 662 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLN F 667 " --> pdb=" O LEU F 663 " (cutoff:3.500A) Processing helix chain 'F' and resid 673 through 675 No H-bonds generated for 'chain 'F' and resid 673 through 675' Processing helix chain 'F' and resid 677 through 682 Processing helix chain 'F' and resid 690 through 706 Proline residue: F 702 - end of helix Processing helix chain 'F' and resid 740 through 752 Processing sheet with id= A, first strand: chain 'A' and resid 519 through 523 removed outlier: 6.886A pdb=" N LYS A 644 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N PHE A 522 " --> pdb=" O LYS A 644 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL A 646 " --> pdb=" O PHE A 522 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 644 through 647 removed outlier: 3.934A pdb=" N LYS B 644 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL B 624 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU B 521 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ALA B 626 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE B 579 " --> pdb=" O LEU B 625 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ALA B 627 " --> pdb=" O ILE B 579 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE B 581 " --> pdb=" O ALA B 627 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 520 through 523 Processing sheet with id= D, first strand: chain 'C' and resid 543 through 547 removed outlier: 3.697A pdb=" N ALA C 627 " --> pdb=" O ILE C 581 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 519 through 523 removed outlier: 6.517A pdb=" N LYS D 644 " --> pdb=" O LEU D 520 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N PHE D 522 " --> pdb=" O LYS D 644 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N VAL D 646 " --> pdb=" O PHE D 522 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'D' and resid 543 through 547 Processing sheet with id= G, first strand: chain 'E' and resid 519 through 523 removed outlier: 7.180A pdb=" N LYS E 644 " --> pdb=" O LEU E 520 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N PHE E 522 " --> pdb=" O LYS E 644 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N VAL E 646 " --> pdb=" O PHE E 522 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'E' and resid 543 through 547 Processing sheet with id= I, first strand: chain 'F' and resid 644 through 647 removed outlier: 3.638A pdb=" N LEU F 520 " --> pdb=" O LYS F 644 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL F 624 " --> pdb=" O LEU F 519 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N LEU F 521 " --> pdb=" O VAL F 624 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ALA F 626 " --> pdb=" O LEU F 521 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE F 581 " --> pdb=" O LEU F 625 " (cutoff:3.500A) 457 hydrogen bonds defined for protein. 1344 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: 3.90 Time building geometry restraints manager: 6.20 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: 4680 1.34 - 1.45: 1647 1.45 - 1.57: 7861 1.57 - 1.69: 33 1.69 - 1.81: 45 Bond restraints: 14266 Sorted by residual: bond pdb=" C4 ATP E 801 " pdb=" C5 ATP E 801 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.08e+01 bond pdb=" C4 AATP F 801 " pdb=" C5 AATP F 801 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 6.00e+01 bond pdb=" C4 ATP D 801 " pdb=" C5 ATP D 801 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.24e+01 bond pdb=" C4 ATP C 801 " pdb=" C5 ATP C 801 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.17e+01 bond pdb=" C4 ATP B 801 " pdb=" C5 ATP B 801 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.08e+01 ... (remaining 14261 not shown) Histogram of bond angle deviations from ideal: 99.10 - 106.70: 426 106.70 - 114.29: 8371 114.29 - 121.89: 7423 121.89 - 129.49: 3048 129.49 - 137.09: 77 Bond angle restraints: 19345 Sorted by residual: angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 114.66 25.21 1.00e+00 1.00e+00 6.36e+02 angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 112.43 24.40 1.00e+00 1.00e+00 5.95e+02 angle pdb=" PB ATP E 801 " pdb=" O3B ATP E 801 " pdb=" PG ATP E 801 " ideal model delta sigma weight residual 139.87 116.84 23.03 1.00e+00 1.00e+00 5.30e+02 angle pdb=" PB ATP B 801 " pdb=" O3B ATP B 801 " pdb=" PG ATP B 801 " ideal model delta sigma weight residual 139.87 117.99 21.88 1.00e+00 1.00e+00 4.79e+02 angle pdb=" PA ATP E 801 " pdb=" O3A ATP E 801 " pdb=" PB ATP E 801 " ideal model delta sigma weight residual 136.83 115.38 21.45 1.00e+00 1.00e+00 4.60e+02 ... (remaining 19340 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.05: 8585 20.05 - 40.10: 285 40.10 - 60.15: 42 60.15 - 80.21: 12 80.21 - 100.26: 6 Dihedral angle restraints: 8930 sinusoidal: 3733 harmonic: 5197 Sorted by residual: dihedral pdb=" CA ASN E 527 " pdb=" C ASN E 527 " pdb=" N GLY E 528 " pdb=" CA GLY E 528 " ideal model delta harmonic sigma weight residual 180.00 151.23 28.77 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" O1BBADP F 802 " pdb=" O3ABADP F 802 " pdb=" PB BADP F 802 " pdb=" PA BADP F 802 " ideal model delta sinusoidal sigma weight residual -60.00 -160.26 100.26 1 2.00e+01 2.50e-03 2.83e+01 dihedral pdb=" CA MET B 574 " pdb=" C MET B 574 " pdb=" N GLN B 575 " pdb=" CA GLN B 575 " ideal model delta harmonic sigma weight residual 180.00 -155.37 -24.63 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 8927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1380 0.036 - 0.072: 598 0.072 - 0.108: 205 0.108 - 0.144: 63 0.144 - 0.180: 8 Chirality restraints: 2254 Sorted by residual: chirality pdb=" C2' ATP D 801 " pdb=" C1' ATP D 801 " pdb=" C3' ATP D 801 " pdb=" O2' ATP D 801 " both_signs ideal model delta sigma weight residual False -2.68 -2.50 -0.18 2.00e-01 2.50e+01 8.14e-01 chirality pdb=" C2' ATP B 801 " pdb=" C1' ATP B 801 " pdb=" C3' ATP B 801 " pdb=" O2' ATP B 801 " both_signs ideal model delta sigma weight residual False -2.68 -2.52 -0.16 2.00e-01 2.50e+01 6.61e-01 chirality pdb=" C2' ATP E 801 " pdb=" C1' ATP E 801 " pdb=" C3' ATP E 801 " pdb=" O2' ATP E 801 " both_signs ideal model delta sigma weight residual False -2.68 -2.52 -0.16 2.00e-01 2.50e+01 6.23e-01 ... (remaining 2251 not shown) Planarity restraints: 2491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 750 " 0.035 2.00e-02 2.50e+03 6.83e-02 4.67e+01 pdb=" C SER B 750 " -0.118 2.00e-02 2.50e+03 pdb=" O SER B 750 " 0.044 2.00e-02 2.50e+03 pdb=" N GLN B 751 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 750 " -0.034 2.00e-02 2.50e+03 6.74e-02 4.55e+01 pdb=" C SER E 750 " 0.117 2.00e-02 2.50e+03 pdb=" O SER E 750 " -0.044 2.00e-02 2.50e+03 pdb=" N GLN E 751 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 753 " 0.034 2.00e-02 2.50e+03 6.55e-02 4.29e+01 pdb=" C TYR C 753 " -0.113 2.00e-02 2.50e+03 pdb=" O TYR C 753 " 0.042 2.00e-02 2.50e+03 pdb=" N GLY C 754 " 0.038 2.00e-02 2.50e+03 ... (remaining 2488 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 168 2.58 - 3.16: 12312 3.16 - 3.74: 20831 3.74 - 4.32: 29221 4.32 - 4.90: 48786 Nonbonded interactions: 111318 Sorted by model distance: nonbonded pdb=" OG1 THR A 543 " pdb=" O SER A 577 " model vdw 1.998 2.440 nonbonded pdb=" O2B ATP A 801 " pdb="MG MG A 802 " model vdw 2.007 2.170 nonbonded pdb=" O2B ATP C 801 " pdb="MG MG C 802 " model vdw 2.010 2.170 nonbonded pdb=" O3G ATP D 801 " pdb="MG MG D 802 " model vdw 2.016 2.170 nonbonded pdb=" O3BBADP F 802 " pdb="MG MG F 803 " model vdw 2.034 2.170 ... (remaining 111313 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 460 through 706 or (resid 707 through 733 and (name N or n \ ame CA or name C or name O or name CB )) or resid 734 through 751)) selection = (chain 'B' and (resid 460 through 501 or resid 517 through 577 or (resid 578 and \ (name N or name CA or name C or name O or name CB )) or resid 579 through 612 o \ r resid 620 through 706 or (resid 707 through 733 and (name N or name CA or name \ C or name O or name CB )) or resid 734 through 751)) selection = (chain 'C' and (resid 460 through 501 or resid 517 through 577 or (resid 578 and \ (name N or name CA or name C or name O or name CB )) or resid 579 through 612 o \ r resid 620 through 706 or (resid 707 through 733 and (name N or name CA or name \ C or name O or name CB )) or resid 734 through 751)) selection = (chain 'D' and (resid 460 through 501 or resid 517 through 577 or (resid 578 and \ (name N or name CA or name C or name O or name CB )) or resid 579 through 612 o \ r resid 620 through 706 or (resid 707 through 733 and (name N or name CA or name \ C or name O or name CB )) or resid 734 through 751)) selection = (chain 'E' and (resid 460 through 501 or resid 517 through 577 or (resid 578 and \ (name N or name CA or name C or name O or name CB )) or resid 579 through 612 o \ r resid 620 through 706 or (resid 707 through 733 and (name N or name CA or name \ C or name O or name CB )) or resid 734 through 751)) selection = (chain 'F' and (resid 460 through 501 or resid 517 through 577 or (resid 578 and \ (name N or name CA or name C or name O or name CB )) or resid 579 through 612 o \ r resid 620 through 751)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 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: 4.420 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 40.570 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.070 ------------------------------------------------------------------------------- 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 : 0.008 0.078 14266 Z= 0.563 Angle : 1.086 25.212 19345 Z= 0.777 Chirality : 0.046 0.180 2254 Planarity : 0.006 0.068 2491 Dihedral : 10.821 100.257 5548 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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: -3.52 (0.17), residues: 1777 helix: -1.94 (0.15), residues: 838 sheet: -2.74 (0.33), residues: 187 loop : -2.55 (0.20), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 749 HIS 0.010 0.002 HIS A 596 PHE 0.019 0.003 PHE A 522 TYR 0.022 0.002 TYR D 686 ARG 0.010 0.001 ARG D 640 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 471 ASP cc_start: 0.7561 (m-30) cc_final: 0.7322 (m-30) REVERT: D 604 THR cc_start: 0.8873 (m) cc_final: 0.8652 (m) REVERT: E 636 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7248 (pt0) REVERT: E 678 ARG cc_start: 0.7860 (mtm-85) cc_final: 0.7652 (ptp-170) REVERT: E 724 GLU cc_start: 0.7464 (tt0) cc_final: 0.6343 (tt0) REVERT: F 517 LYS cc_start: 0.7453 (mtmt) cc_final: 0.7183 (mtpt) REVERT: F 582 ASP cc_start: 0.7193 (m-30) cc_final: 0.6727 (m-30) REVERT: F 681 LYS cc_start: 0.4313 (mtpp) cc_final: 0.3985 (pttt) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.3620 time to fit residues: 137.2240 Evaluate side-chains 124 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 72 optimal weight: 0.0270 chunk 139 optimal weight: 0.9980 chunk 53 optimal weight: 0.0010 chunk 84 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 overall best weight: 0.4644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN A 546 ASN A 596 HIS B 575 GLN ** B 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 707 ASN B 710 GLN ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 ASN D 583 GLN D 596 HIS D 629 ASN E 575 GLN E 596 HIS F 596 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14266 Z= 0.179 Angle : 0.585 8.367 19345 Z= 0.279 Chirality : 0.043 0.154 2254 Planarity : 0.004 0.048 2491 Dihedral : 11.431 84.768 2159 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.94 % Allowed : 7.64 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.62 (0.19), residues: 1777 helix: -0.31 (0.17), residues: 834 sheet: -2.04 (0.34), residues: 182 loop : -1.61 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 749 HIS 0.002 0.001 HIS C 596 PHE 0.021 0.001 PHE C 610 TYR 0.013 0.001 TYR A 746 ARG 0.007 0.001 ARG B 677 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 162 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 473 ILE cc_start: 0.8235 (mt) cc_final: 0.7991 (pt) REVERT: A 682 ILE cc_start: 0.8622 (mt) cc_final: 0.8371 (mt) REVERT: B 471 ASP cc_start: 0.7497 (m-30) cc_final: 0.7272 (m-30) REVERT: B 616 ASN cc_start: 0.8436 (t0) cc_final: 0.7823 (t0) REVERT: B 719 MET cc_start: 0.7331 (tpp) cc_final: 0.7114 (ttt) REVERT: E 636 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7186 (pt0) REVERT: E 678 ARG cc_start: 0.7830 (mtm-85) cc_final: 0.7545 (ptp-170) REVERT: E 712 LYS cc_start: 0.8039 (mttt) cc_final: 0.7746 (mtmt) REVERT: E 724 GLU cc_start: 0.7428 (tt0) cc_final: 0.6331 (tt0) REVERT: F 681 LYS cc_start: 0.4017 (mtpp) cc_final: 0.3742 (pttt) outliers start: 14 outliers final: 6 residues processed: 169 average time/residue: 0.3109 time to fit residues: 75.3421 Evaluate side-chains 126 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 120 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain E residue 682 ILE Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain F residue 464 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 174 optimal weight: 0.4980 chunk 144 optimal weight: 8.9990 chunk 160 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 129 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN B 654 GLN ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14266 Z= 0.182 Angle : 0.540 6.636 19345 Z= 0.261 Chirality : 0.042 0.147 2254 Planarity : 0.004 0.043 2491 Dihedral : 10.620 85.501 2159 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.54 % Allowed : 8.91 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.20), residues: 1777 helix: 0.39 (0.18), residues: 833 sheet: -1.54 (0.35), residues: 182 loop : -1.18 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 749 HIS 0.003 0.001 HIS C 596 PHE 0.013 0.001 PHE C 610 TYR 0.009 0.001 TYR D 647 ARG 0.005 0.000 ARG C 735 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 138 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 LEU cc_start: 0.9238 (tm) cc_final: 0.9004 (tm) REVERT: B 471 ASP cc_start: 0.7517 (m-30) cc_final: 0.7273 (m-30) REVERT: B 616 ASN cc_start: 0.8481 (t0) cc_final: 0.7892 (t0) REVERT: D 690 ASP cc_start: 0.7521 (m-30) cc_final: 0.7317 (m-30) REVERT: E 636 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7200 (pt0) REVERT: E 719 MET cc_start: 0.7280 (tpp) cc_final: 0.6880 (tpt) REVERT: E 724 GLU cc_start: 0.7494 (tt0) cc_final: 0.7240 (tt0) REVERT: F 630 ARG cc_start: 0.8427 (mtt-85) cc_final: 0.7956 (mpp80) REVERT: F 657 GLU cc_start: 0.7503 (tt0) cc_final: 0.6867 (mt-10) outliers start: 23 outliers final: 10 residues processed: 154 average time/residue: 0.2813 time to fit residues: 63.3684 Evaluate side-chains 130 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 120 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain D residue 585 ASP Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain F residue 659 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 172 optimal weight: 7.9990 chunk 154 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 654 GLN ** B 707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 HIS ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14266 Z= 0.334 Angle : 0.626 8.041 19345 Z= 0.304 Chirality : 0.045 0.164 2254 Planarity : 0.004 0.052 2491 Dihedral : 10.621 82.320 2159 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.14 % Allowed : 9.38 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.20), residues: 1777 helix: 0.63 (0.18), residues: 826 sheet: -1.18 (0.36), residues: 192 loop : -1.08 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 749 HIS 0.005 0.001 HIS C 596 PHE 0.020 0.002 PHE D 642 TYR 0.015 0.002 TYR B 686 ARG 0.007 0.001 ARG F 534 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 136 time to evaluate : 1.660 Fit side-chains revert: symmetry clash REVERT: A 519 LEU cc_start: 0.9240 (tm) cc_final: 0.9026 (tm) REVERT: B 616 ASN cc_start: 0.8475 (t0) cc_final: 0.7923 (t0) REVERT: D 662 ARG cc_start: 0.8012 (ttm110) cc_final: 0.7534 (ttp-110) REVERT: E 605 GLU cc_start: 0.8412 (tp30) cc_final: 0.8193 (tp30) REVERT: E 719 MET cc_start: 0.7285 (tpp) cc_final: 0.6920 (tpt) REVERT: F 657 GLU cc_start: 0.7568 (tt0) cc_final: 0.7012 (mt-10) REVERT: F 676 LEU cc_start: 0.4951 (OUTLIER) cc_final: 0.4306 (pp) REVERT: G 9 GLU cc_start: 0.7559 (pt0) cc_final: 0.7275 (pt0) outliers start: 32 outliers final: 23 residues processed: 160 average time/residue: 0.2673 time to fit residues: 63.3647 Evaluate side-chains 137 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 113 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain D residue 585 ASP Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain E residue 559 ASP Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 682 ILE Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain F residue 527 ASN Chi-restraints excluded: chain F residue 659 LEU Chi-restraints excluded: chain F residue 676 LEU Chi-restraints excluded: chain F residue 689 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 0.0980 chunk 154 optimal weight: 9.9990 chunk 43 optimal weight: 0.0570 chunk 57 optimal weight: 0.0570 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN B 575 GLN ** B 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 14266 Z= 0.133 Angle : 0.510 7.165 19345 Z= 0.243 Chirality : 0.040 0.146 2254 Planarity : 0.003 0.045 2491 Dihedral : 10.296 88.564 2159 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.68 % Allowed : 11.80 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.21), residues: 1777 helix: 1.03 (0.19), residues: 831 sheet: -0.67 (0.38), residues: 184 loop : -0.87 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 749 HIS 0.001 0.000 HIS D 728 PHE 0.010 0.001 PHE C 610 TYR 0.007 0.001 TYR C 753 ARG 0.005 0.000 ARG E 678 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 137 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LEU cc_start: 0.7808 (tp) cc_final: 0.7589 (tp) REVERT: B 616 ASN cc_start: 0.8489 (t0) cc_final: 0.7906 (t0) REVERT: C 636 GLU cc_start: 0.7956 (pm20) cc_final: 0.7748 (pm20) REVERT: D 662 ARG cc_start: 0.7927 (ttm110) cc_final: 0.7473 (ttp-110) REVERT: E 605 GLU cc_start: 0.8412 (tp30) cc_final: 0.8189 (tp30) REVERT: E 712 LYS cc_start: 0.7986 (mttm) cc_final: 0.7524 (mtmt) REVERT: E 719 MET cc_start: 0.7367 (tpp) cc_final: 0.7006 (tpt) REVERT: F 630 ARG cc_start: 0.8475 (mtt-85) cc_final: 0.7946 (mpp80) REVERT: F 657 GLU cc_start: 0.7563 (tt0) cc_final: 0.7084 (mt-10) REVERT: F 676 LEU cc_start: 0.5036 (OUTLIER) cc_final: 0.4246 (pp) outliers start: 25 outliers final: 13 residues processed: 151 average time/residue: 0.2868 time to fit residues: 63.7002 Evaluate side-chains 131 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 117 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain E residue 574 MET Chi-restraints excluded: chain F residue 659 LEU Chi-restraints excluded: chain F residue 676 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 172 optimal weight: 20.0000 chunk 142 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 90 optimal weight: 0.2980 chunk 166 optimal weight: 4.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 ASN E 728 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 14266 Z= 0.381 Angle : 0.628 7.909 19345 Z= 0.305 Chirality : 0.045 0.158 2254 Planarity : 0.004 0.045 2491 Dihedral : 10.322 88.087 2159 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.28 % Allowed : 12.06 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.20), residues: 1777 helix: 0.90 (0.18), residues: 820 sheet: -1.00 (0.36), residues: 201 loop : -0.85 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 749 HIS 0.003 0.001 HIS D 596 PHE 0.014 0.002 PHE E 544 TYR 0.014 0.002 TYR D 647 ARG 0.004 0.001 ARG F 600 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 121 time to evaluate : 1.748 Fit side-chains revert: symmetry clash REVERT: A 468 LEU cc_start: 0.7977 (tp) cc_final: 0.7748 (tp) REVERT: B 616 ASN cc_start: 0.8604 (t0) cc_final: 0.7975 (t0) REVERT: C 616 ASN cc_start: 0.8214 (t0) cc_final: 0.7920 (t0) REVERT: C 748 LYS cc_start: 0.8371 (ttpt) cc_final: 0.8072 (tppt) REVERT: E 719 MET cc_start: 0.7247 (tpp) cc_final: 0.6976 (tpt) REVERT: F 657 GLU cc_start: 0.7653 (tt0) cc_final: 0.7134 (mt-10) outliers start: 34 outliers final: 28 residues processed: 144 average time/residue: 0.2676 time to fit residues: 57.7568 Evaluate side-chains 130 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 102 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 713 CYS Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain D residue 585 ASP Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 744 ASN Chi-restraints excluded: chain E residue 559 ASP Chi-restraints excluded: chain E residue 574 MET Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 618 ASP Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain F residue 498 MET Chi-restraints excluded: chain F residue 592 SER Chi-restraints excluded: chain F residue 659 LEU Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain G residue 12 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 125 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 171 optimal weight: 0.2980 chunk 107 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 728 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14266 Z= 0.172 Angle : 0.524 7.351 19345 Z= 0.250 Chirality : 0.041 0.147 2254 Planarity : 0.003 0.045 2491 Dihedral : 10.107 83.302 2159 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.68 % Allowed : 13.00 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.21), residues: 1777 helix: 1.13 (0.19), residues: 822 sheet: -0.52 (0.38), residues: 187 loop : -0.76 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 749 HIS 0.002 0.000 HIS D 573 PHE 0.008 0.001 PHE F 580 TYR 0.009 0.001 TYR D 647 ARG 0.005 0.000 ARG D 621 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 122 time to evaluate : 1.697 Fit side-chains revert: symmetry clash REVERT: B 616 ASN cc_start: 0.8604 (t0) cc_final: 0.7948 (t0) REVERT: C 748 LYS cc_start: 0.8278 (ttpt) cc_final: 0.8020 (tppt) REVERT: E 613 LEU cc_start: 0.8691 (mp) cc_final: 0.8474 (mp) REVERT: E 719 MET cc_start: 0.7238 (tpp) cc_final: 0.6976 (tpt) REVERT: F 630 ARG cc_start: 0.8568 (mtt-85) cc_final: 0.8092 (mpp80) REVERT: F 657 GLU cc_start: 0.7481 (tt0) cc_final: 0.7006 (mt-10) outliers start: 25 outliers final: 21 residues processed: 136 average time/residue: 0.2556 time to fit residues: 52.3700 Evaluate side-chains 128 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 697 ASP Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 744 ASN Chi-restraints excluded: chain D residue 753 TYR Chi-restraints excluded: chain E residue 559 ASP Chi-restraints excluded: chain E residue 574 MET Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain F residue 659 LEU Chi-restraints excluded: chain G residue 12 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 156 optimal weight: 0.0470 chunk 164 optimal weight: 0.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14266 Z= 0.206 Angle : 0.528 6.953 19345 Z= 0.254 Chirality : 0.041 0.143 2254 Planarity : 0.003 0.046 2491 Dihedral : 9.937 82.027 2159 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.14 % Allowed : 12.87 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.21), residues: 1777 helix: 1.25 (0.19), residues: 819 sheet: -0.40 (0.38), residues: 187 loop : -0.72 (0.23), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 749 HIS 0.002 0.000 HIS F 573 PHE 0.009 0.001 PHE A 568 TYR 0.009 0.001 TYR D 647 ARG 0.005 0.000 ARG D 621 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 109 time to evaluate : 1.692 Fit side-chains revert: symmetry clash REVERT: B 548 SER cc_start: 0.8437 (OUTLIER) cc_final: 0.8225 (t) REVERT: B 616 ASN cc_start: 0.8630 (t0) cc_final: 0.7945 (t0) REVERT: C 748 LYS cc_start: 0.8286 (ttpt) cc_final: 0.8034 (tppt) REVERT: E 719 MET cc_start: 0.7285 (tpp) cc_final: 0.7053 (tpt) REVERT: F 657 GLU cc_start: 0.7499 (tt0) cc_final: 0.7062 (mt-10) outliers start: 32 outliers final: 25 residues processed: 128 average time/residue: 0.2742 time to fit residues: 52.8503 Evaluate side-chains 133 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 107 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 713 CYS Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 697 ASP Chi-restraints excluded: chain D residue 585 ASP Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 744 ASN Chi-restraints excluded: chain D residue 753 TYR Chi-restraints excluded: chain E residue 559 ASP Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain F residue 498 MET Chi-restraints excluded: chain F residue 592 SER Chi-restraints excluded: chain F residue 659 LEU Chi-restraints excluded: chain G residue 12 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 151 optimal weight: 0.4980 chunk 104 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 ASN ** E 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14266 Z= 0.195 Angle : 0.520 6.685 19345 Z= 0.250 Chirality : 0.041 0.145 2254 Planarity : 0.003 0.045 2491 Dihedral : 9.871 82.209 2159 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.88 % Allowed : 13.00 % Favored : 85.12 % 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: 0.41 (0.21), residues: 1777 helix: 1.28 (0.19), residues: 824 sheet: -0.30 (0.38), residues: 186 loop : -0.65 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 749 HIS 0.001 0.000 HIS D 573 PHE 0.008 0.001 PHE E 544 TYR 0.009 0.001 TYR D 647 ARG 0.005 0.000 ARG D 621 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 117 time to evaluate : 1.555 Fit side-chains revert: symmetry clash REVERT: B 616 ASN cc_start: 0.8647 (t0) cc_final: 0.7932 (t0) REVERT: C 748 LYS cc_start: 0.8267 (ttpt) cc_final: 0.8024 (tppt) REVERT: E 719 MET cc_start: 0.7266 (tpp) cc_final: 0.7027 (tpt) REVERT: F 657 GLU cc_start: 0.7448 (tt0) cc_final: 0.7020 (mt-10) outliers start: 28 outliers final: 25 residues processed: 136 average time/residue: 0.2679 time to fit residues: 54.6694 Evaluate side-chains 132 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 713 CYS Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 697 ASP Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 744 ASN Chi-restraints excluded: chain D residue 753 TYR Chi-restraints excluded: chain E residue 559 ASP Chi-restraints excluded: chain E residue 574 MET Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 673 THR Chi-restraints excluded: chain F residue 498 MET Chi-restraints excluded: chain F residue 592 SER Chi-restraints excluded: chain F residue 659 LEU Chi-restraints excluded: chain G residue 12 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 0.0020 chunk 80 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 177 optimal weight: 6.9990 chunk 163 optimal weight: 7.9990 chunk 141 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 112 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 overall best weight: 1.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 ASN ** E 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14266 Z= 0.223 Angle : 0.537 9.523 19345 Z= 0.258 Chirality : 0.042 0.153 2254 Planarity : 0.003 0.046 2491 Dihedral : 9.855 82.249 2159 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.88 % Allowed : 13.81 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.21), residues: 1777 helix: 1.34 (0.19), residues: 814 sheet: -0.33 (0.38), residues: 188 loop : -0.63 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 749 HIS 0.001 0.001 HIS F 596 PHE 0.024 0.001 PHE A 580 TYR 0.009 0.001 TYR D 647 ARG 0.005 0.000 ARG D 621 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 109 time to evaluate : 1.660 Fit side-chains revert: symmetry clash REVERT: B 616 ASN cc_start: 0.8617 (t0) cc_final: 0.7854 (t0) REVERT: E 719 MET cc_start: 0.7271 (tpp) cc_final: 0.7037 (tpt) REVERT: F 657 GLU cc_start: 0.7473 (tt0) cc_final: 0.7043 (mt-10) outliers start: 28 outliers final: 27 residues processed: 127 average time/residue: 0.2715 time to fit residues: 52.3841 Evaluate side-chains 134 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 107 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 713 CYS Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 697 ASP Chi-restraints excluded: chain D residue 585 ASP Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 744 ASN Chi-restraints excluded: chain D residue 753 TYR Chi-restraints excluded: chain E residue 559 ASP Chi-restraints excluded: chain E residue 574 MET Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 673 THR Chi-restraints excluded: chain F residue 498 MET Chi-restraints excluded: chain F residue 592 SER Chi-restraints excluded: chain F residue 659 LEU Chi-restraints excluded: chain F residue 689 SER Chi-restraints excluded: chain G residue 12 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 145 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 124 optimal weight: 0.0970 chunk 8 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 527 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 = 0.3722 r_free = 0.3722 target = 0.133108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.098239 restraints weight = 21060.101| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.78 r_work: 0.3088 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14266 Z= 0.165 Angle : 0.512 8.003 19345 Z= 0.245 Chirality : 0.041 0.144 2254 Planarity : 0.003 0.047 2491 Dihedral : 9.754 82.847 2159 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.54 % Allowed : 14.48 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.21), residues: 1777 helix: 1.44 (0.19), residues: 816 sheet: -0.19 (0.38), residues: 188 loop : -0.56 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 749 HIS 0.001 0.000 HIS D 573 PHE 0.020 0.001 PHE A 580 TYR 0.009 0.001 TYR D 647 ARG 0.005 0.000 ARG D 621 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2876.87 seconds wall clock time: 53 minutes 18.17 seconds (3198.17 seconds total)