Starting phenix.real_space_refine on Mon Jan 13 21:53:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bcp_44433/01_2025/9bcp_44433.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bcp_44433/01_2025/9bcp_44433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bcp_44433/01_2025/9bcp_44433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bcp_44433/01_2025/9bcp_44433.map" model { file = "/net/cci-nas-00/data/ceres_data/9bcp_44433/01_2025/9bcp_44433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bcp_44433/01_2025/9bcp_44433.cif" } resolution = 4.1 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= 0.058 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 12 5.16 5 C 2594 2.51 5 N 779 2.21 5 O 771 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 4162 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2008 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 136} Link IDs: {'PTRANS': 15, 'TRANS': 288} Chain breaks: 1 Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 601 Unresolved non-hydrogen dihedrals: 367 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 20, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 275 Chain: "A" Number of atoms: 2091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2091 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 137} Link IDs: {'PTRANS': 15, 'TRANS': 298} Chain breaks: 1 Unresolved non-hydrogen bonds: 465 Unresolved non-hydrogen angles: 584 Unresolved non-hydrogen dihedrals: 363 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 11, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 20, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 254 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.45, per 1000 atoms: 1.07 Number of scatterers: 4162 At special positions: 0 Unit cell: (81.3, 112.736, 67.208, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 6 15.00 O 771 8.00 N 779 7.00 C 2594 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 - 3.00 Amino acid : True - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 631.5 milliseconds 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1170 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 2 sheets defined 46.9% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'B' and resid 545 through 557 Processing helix chain 'B' and resid 587 through 594 removed outlier: 3.530A pdb=" N ASN B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 620 removed outlier: 3.816A pdb=" N ILE B 611 " --> pdb=" O LEU B 607 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN B 620 " --> pdb=" O LEU B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 666 removed outlier: 3.535A pdb=" N LYS B 666 " --> pdb=" O THR B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 676 Processing helix chain 'B' and resid 685 through 703 Processing helix chain 'B' and resid 715 through 725 Processing helix chain 'B' and resid 741 through 751 removed outlier: 4.321A pdb=" N GLY B 745 " --> pdb=" O LEU B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 773 Processing helix chain 'B' and resid 774 through 776 No H-bonds generated for 'chain 'B' and resid 774 through 776' Processing helix chain 'B' and resid 781 through 809 removed outlier: 3.962A pdb=" N MET B 788 " --> pdb=" O LEU B 784 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU B 789 " --> pdb=" O LEU B 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 558 Processing helix chain 'A' and resid 587 through 594 removed outlier: 3.732A pdb=" N ASN A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 619 removed outlier: 3.738A pdb=" N PHE A 617 " --> pdb=" O LYS A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 removed outlier: 4.031A pdb=" N CYS A 634 " --> pdb=" O SER A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 668 removed outlier: 3.978A pdb=" N LEU A 668 " --> pdb=" O TYR A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 677 removed outlier: 3.575A pdb=" N LEU A 675 " --> pdb=" O ALA A 671 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 702 Processing helix chain 'A' and resid 715 through 726 Processing helix chain 'A' and resid 741 through 752 Processing helix chain 'A' and resid 761 through 773 Processing helix chain 'A' and resid 780 through 810 removed outlier: 4.086A pdb=" N LEU A 784 " --> pdb=" O ILE A 780 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 524 through 527 removed outlier: 5.771A pdb=" N GLU B 581 " --> pdb=" O PHE B 566 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N PHE B 566 " --> pdb=" O GLU B 581 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 525 through 526 removed outlier: 3.554A pdb=" N CYS A 577 " --> pdb=" O CYS A 570 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY A 568 " --> pdb=" O LEU A 579 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLU A 581 " --> pdb=" O PHE A 566 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N PHE A 566 " --> pdb=" O GLU A 581 " (cutoff:3.500A) 206 hydrogen bonds defined for protein. 609 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: 1.13 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 704 1.31 - 1.43: 1114 1.43 - 1.56: 2405 1.56 - 1.68: 8 1.68 - 1.81: 18 Bond restraints: 4249 Sorted by residual: bond pdb=" C4 ATP B1101 " pdb=" C5 ATP B1101 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.10e+01 bond pdb=" C5 ATP B1101 " pdb=" C6 ATP B1101 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.95e+01 bond pdb=" C8 ATP B1101 " pdb=" N7 ATP B1101 " ideal model delta sigma weight residual 1.310 1.357 -0.047 1.00e-02 1.00e+04 2.21e+01 bond pdb=" C1' ATP A1101 " pdb=" N9 ATP A1101 " ideal model delta sigma weight residual 1.459 1.397 0.062 1.40e-02 5.10e+03 1.93e+01 bond pdb=" C5 ATP B1101 " pdb=" N7 ATP B1101 " ideal model delta sigma weight residual 1.387 1.343 0.044 1.00e-02 1.00e+04 1.91e+01 ... (remaining 4244 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.28: 5814 5.28 - 10.56: 19 10.56 - 15.84: 1 15.84 - 21.12: 3 21.12 - 26.41: 2 Bond angle restraints: 5839 Sorted by residual: angle pdb=" PB ATP A1101 " pdb=" O3B ATP A1101 " pdb=" PG ATP A1101 " ideal model delta sigma weight residual 139.87 113.46 26.41 1.00e+00 1.00e+00 6.97e+02 angle pdb=" PA ATP A1101 " pdb=" O3A ATP A1101 " pdb=" PB ATP A1101 " ideal model delta sigma weight residual 136.83 115.13 21.70 1.00e+00 1.00e+00 4.71e+02 angle pdb=" PB ATP B1101 " pdb=" O3B ATP B1101 " pdb=" PG ATP B1101 " ideal model delta sigma weight residual 139.87 120.71 19.16 1.00e+00 1.00e+00 3.67e+02 angle pdb=" PA ATP B1101 " pdb=" O3A ATP B1101 " pdb=" PB ATP B1101 " ideal model delta sigma weight residual 136.83 118.16 18.67 1.00e+00 1.00e+00 3.48e+02 angle pdb=" C GLN A 790 " pdb=" CA GLN A 790 " pdb=" CB GLN A 790 " ideal model delta sigma weight residual 110.70 129.71 -19.01 1.83e+00 2.99e-01 1.08e+02 ... (remaining 5834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 2331 17.81 - 35.61: 162 35.61 - 53.42: 41 53.42 - 71.23: 8 71.23 - 89.03: 10 Dihedral angle restraints: 2552 sinusoidal: 753 harmonic: 1799 Sorted by residual: dihedral pdb=" C GLN A 790 " pdb=" N GLN A 790 " pdb=" CA GLN A 790 " pdb=" CB GLN A 790 " ideal model delta harmonic sigma weight residual -122.60 -138.80 16.20 0 2.50e+00 1.60e-01 4.20e+01 dihedral pdb=" CA VAL A 706 " pdb=" C VAL A 706 " pdb=" N PHE A 707 " pdb=" CA PHE A 707 " ideal model delta harmonic sigma weight residual 180.00 154.79 25.21 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA ASP A 600 " pdb=" C ASP A 600 " pdb=" N TRP A 601 " pdb=" CA TRP A 601 " ideal model delta harmonic sigma weight residual 180.00 156.47 23.53 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 2549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 612 0.083 - 0.166: 51 0.166 - 0.249: 3 0.249 - 0.331: 0 0.331 - 0.414: 1 Chirality restraints: 667 Sorted by residual: chirality pdb=" CA GLN A 790 " pdb=" N GLN A 790 " pdb=" C GLN A 790 " pdb=" CB GLN A 790 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.29e+00 chirality pdb=" CA ASN A 633 " pdb=" N ASN A 633 " pdb=" C ASN A 633 " pdb=" CB ASN A 633 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CA VAL A 532 " pdb=" N VAL A 532 " pdb=" C VAL A 532 " pdb=" CB VAL A 532 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.88e-01 ... (remaining 664 not shown) Planarity restraints: 780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 531 " -0.025 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C LEU A 531 " 0.085 2.00e-02 2.50e+03 pdb=" O LEU A 531 " -0.032 2.00e-02 2.50e+03 pdb=" N VAL A 532 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 656 " 0.053 5.00e-02 4.00e+02 7.93e-02 1.01e+01 pdb=" N PRO A 657 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 657 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 657 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 755 " 0.051 5.00e-02 4.00e+02 7.56e-02 9.15e+00 pdb=" N PRO A 756 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 756 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 756 " 0.041 5.00e-02 4.00e+02 ... (remaining 777 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1818 2.89 - 3.39: 4209 3.39 - 3.90: 5859 3.90 - 4.40: 6112 4.40 - 4.90: 9694 Nonbonded interactions: 27692 Sorted by model distance: nonbonded pdb=" O SER A 632 " pdb=" OD1 ASN A 633 " model vdw 2.391 3.040 nonbonded pdb=" O ASN B 773 " pdb=" OD1 ASN B 773 " model vdw 2.399 3.040 nonbonded pdb=" OD1 ASN B 633 " pdb=" O1B ATP B1101 " model vdw 2.405 3.040 nonbonded pdb=" O ASP A 572 " pdb=" O ASN A 575 " model vdw 2.429 3.040 nonbonded pdb=" O PHE A 640 " pdb=" NH1 ARG A 787 " model vdw 2.434 3.120 ... (remaining 27687 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 473 through 478 and (name N or name CA or name C or name \ O or name CB )) or resid 479 through 485 or (resid 486 and (name N or name CA or \ name C or name O or name CB )) or resid 522 through 525 or (resid 526 through 5 \ 27 and (name N or name CA or name C or name O or name CB )) or resid 528 through \ 529 or (resid 530 through 533 and (name N or name CA or name C or name O or nam \ e CB )) or resid 534 through 535 or (resid 536 through 541 and (name N or name C \ A or name C or name O or name CB )) or resid 542 through 545 or (resid 546 throu \ gh 559 and (name N or name CA or name C or name O or name CB )) or resid 560 or \ (resid 561 and (name N or name CA or name C or name O or name CB )) or resid 562 \ or (resid 563 through 567 and (name N or name CA or name C or name O or name CB \ )) or (resid 568 through 572 and (name N or name CA or name C or name O or name \ CB )) or resid 573 through 574 or (resid 575 through 580 and (name N or name CA \ or name C or name O or name CB )) or resid 581 through 600 or (resid 601 throug \ h 602 and (name N or name CA or name C or name O or name CB )) or resid 603 thro \ ugh 606 or (resid 607 through 613 and (name N or name CA or name C or name O or \ name CB )) or resid 614 through 625 or (resid 626 and (name N or name CA or name \ C or name O or name CB )) or resid 627 through 633 or (resid 634 through 637 an \ d (name N or name CA or name C or name O or name CB )) or resid 638 through 661 \ or (resid 662 through 665 and (name N or name CA or name C or name O or name CB \ )) or resid 666 through 667 or (resid 668 and (name N or name CA or name C or na \ me O or name CB )) or resid 669 through 674 or (resid 675 and (name N or name CA \ or name C or name O or name CB )) or resid 676 through 684 or (resid 685 and (n \ ame N or name CA or name C or name O or name CB )) or resid 686 through 688 or ( \ resid 689 through 690 and (name N or name CA or name C or name O or name CB )) o \ r resid 691 through 697 or (resid 698 through 699 and (name N or name CA or name \ C or name O or name CB )) or resid 700 through 713 or (resid 714 through 715 an \ d (name N or name CA or name C or name O or name CB )) or resid 716 through 719 \ or (resid 720 through 722 and (name N or name CA or name C or name O or name CB \ )) or resid 723 through 733 or (resid 734 through 736 and (name N or name CA or \ name C or name O or name CB )) or resid 737 through 742 or (resid 743 and (name \ N or name CA or name C or name O or name CB )) or resid 744 through 750 or (resi \ d 751 and (name N or name CA or name C or name O or name CB )) or resid 752 thro \ ugh 766 or (resid 767 through 768 and (name N or name CA or name C or name O or \ name CB )) or resid 769 or (resid 770 through 780 and (name N or name CA or name \ C or name O or name CB )) or resid 781 through 786 or (resid 787 and (name N or \ name CA or name C or name O or name CB )) or resid 788 through 808 or (resid 80 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 1101)) selection = (chain 'B' and ((resid 473 through 478 and (name N or name CA or name C or name \ O or name CB )) or resid 479 through 530 or (resid 531 through 533 and (name N o \ r name CA or name C or name O or name CB )) or resid 534 or (resid 535 through 5 \ 41 and (name N or name CA or name C or name O or name CB )) or resid 542 through \ 546 or (resid 547 through 559 and (name N or name CA or name C or name O or nam \ e CB )) or resid 560 through 564 or (resid 565 through 567 and (name N or name C \ A or name C or name O or name CB )) or resid 568 through 577 or (resid 578 throu \ gh 580 and (name N or name CA or name C or name O or name CB )) or resid 581 thr \ ough 593 or (resid 594 through 596 and (name N or name CA or name C or name O or \ name CB )) or resid 597 through 599 or (resid 600 through 602 and (name N or na \ me CA or name C or name O or name CB )) or resid 603 through 615 or (resid 616 a \ nd (name N or name CA or name C or name O or name CB )) or resid 617 through 622 \ or (resid 623 and (name N or name CA or name C or name O or name CB )) or resid \ 624 or (resid 625 through 626 and (name N or name CA or name C or name O or nam \ e CB )) or resid 627 through 634 or (resid 635 through 637 and (name N or name C \ A or name C or name O or name CB )) or resid 638 or (resid 639 and (name N or na \ me CA or name C or name O or name CB )) or resid 640 through 642 or (resid 643 a \ nd (name N or name CA or name C or name O or name CB )) or resid 644 through 652 \ or (resid 653 through 654 and (name N or name CA or name C or name O or name CB \ )) or resid 655 through 676 or (resid 677 through 679 and (name N or name CA or \ name C or name O or name CB )) or resid 680 through 682 or (resid 683 and (name \ N or name CA or name C or name O or name CB )) or resid 684 through 691 or (res \ id 692 and (name N or name CA or name C or name O or name CB )) or resid 693 thr \ ough 694 or (resid 695 through 699 and (name N or name CA or name C or name O or \ name CB )) or resid 700 through 703 or (resid 704 and (name N or name CA or nam \ e C or name O or name CB )) or resid 705 through 711 or (resid 712 and (name N o \ r name CA or name C or name O or name CB )) or resid 713 through 727 or (resid 7 \ 28 and (name N or name CA or name C or name O or name CB )) or resid 729 through \ 738 or (resid 739 and (name N or name CA or name C or name O or name CB )) or r \ esid 740 through 772 or (resid 773 through 780 and (name N or name CA or name C \ or name O or name CB )) or resid 781 through 784 or (resid 785 through 787 and ( \ name N or name CA or name C or name O or name CB )) or resid 788 or (resid 789 a \ nd (name N or name CA or name C or name O or name CB )) or resid 790 through 799 \ or (resid 800 through 801 and (name N or name CA or name C or name O or name CB \ )) or resid 802 through 809 or resid 1101)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.730 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.030 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 4249 Z= 0.407 Angle : 1.105 26.405 5839 Z= 0.819 Chirality : 0.047 0.414 667 Planarity : 0.006 0.079 780 Dihedral : 15.684 89.033 1382 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 0.35 % Allowed : 1.06 % Favored : 98.58 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.31), residues: 610 helix: -0.24 (0.30), residues: 264 sheet: -0.23 (1.38), residues: 17 loop : -3.56 (0.30), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 752 HIS 0.009 0.002 HIS A 491 PHE 0.014 0.002 PHE B 693 TYR 0.034 0.003 TYR A 691 ARG 0.010 0.001 ARG B 639 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: B 615 MET cc_start: 0.8472 (mmm) cc_final: 0.8215 (tpp) REVERT: B 666 LYS cc_start: 0.6790 (OUTLIER) cc_final: 0.6560 (tmmt) REVERT: B 731 PHE cc_start: 0.7882 (t80) cc_final: 0.7256 (t80) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.1520 time to fit residues: 17.6213 Evaluate side-chains 59 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.4980 chunk 46 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 0.2980 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 633 ASN A 633 ASN A 757 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.143853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.125389 restraints weight = 10394.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.127943 restraints weight = 7292.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.129803 restraints weight = 5538.074| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4249 Z= 0.218 Angle : 0.653 6.708 5839 Z= 0.358 Chirality : 0.041 0.148 667 Planarity : 0.005 0.056 780 Dihedral : 11.467 84.609 724 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.71 % Allowed : 4.61 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.32), residues: 610 helix: 0.49 (0.30), residues: 267 sheet: -2.02 (1.04), residues: 27 loop : -2.93 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 752 HIS 0.007 0.002 HIS A 491 PHE 0.018 0.002 PHE A 693 TYR 0.027 0.002 TYR B 605 ARG 0.004 0.000 ARG B 585 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: B 581 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8283 (mt-10) REVERT: A 530 ASN cc_start: 0.6848 (t0) cc_final: 0.6494 (t0) REVERT: A 634 CYS cc_start: 0.7086 (p) cc_final: 0.6531 (p) REVERT: A 788 MET cc_start: 0.8377 (mmp) cc_final: 0.8037 (mmp) outliers start: 2 outliers final: 0 residues processed: 79 average time/residue: 0.1200 time to fit residues: 12.8438 Evaluate side-chains 58 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 5 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 15 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 36 optimal weight: 0.0570 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 773 ASN A 757 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.146428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.127749 restraints weight = 10125.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.130421 restraints weight = 6997.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.132441 restraints weight = 5249.823| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4249 Z= 0.165 Angle : 0.575 5.969 5839 Z= 0.307 Chirality : 0.040 0.147 667 Planarity : 0.005 0.047 780 Dihedral : 10.849 78.441 724 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.35 % Allowed : 4.61 % Favored : 95.04 % 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: -1.27 (0.34), residues: 610 helix: 1.04 (0.31), residues: 269 sheet: -2.04 (1.02), residues: 27 loop : -2.58 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 752 HIS 0.005 0.001 HIS B 708 PHE 0.010 0.002 PHE A 693 TYR 0.021 0.002 TYR B 605 ARG 0.002 0.000 ARG B 604 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.526 Fit side-chains REVERT: B 562 HIS cc_start: 0.8191 (m90) cc_final: 0.7879 (m90) REVERT: B 581 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8231 (mt-10) REVERT: B 731 PHE cc_start: 0.7907 (t80) cc_final: 0.7256 (t80) REVERT: A 530 ASN cc_start: 0.6710 (t0) cc_final: 0.6334 (t0) REVERT: A 634 CYS cc_start: 0.7014 (p) cc_final: 0.6406 (p) REVERT: A 788 MET cc_start: 0.8475 (mmp) cc_final: 0.8137 (mmm) outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.1316 time to fit residues: 13.3702 Evaluate side-chains 60 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 46 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 42 optimal weight: 0.0070 chunk 49 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 633 ASN A 757 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.148691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.129802 restraints weight = 10210.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.132558 restraints weight = 7024.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.134636 restraints weight = 5213.788| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4249 Z= 0.160 Angle : 0.556 5.978 5839 Z= 0.296 Chirality : 0.039 0.147 667 Planarity : 0.005 0.044 780 Dihedral : 10.446 77.840 724 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % 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: -0.93 (0.35), residues: 610 helix: 1.28 (0.32), residues: 270 sheet: -1.88 (1.03), residues: 27 loop : -2.36 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 601 HIS 0.003 0.001 HIS A 661 PHE 0.013 0.001 PHE A 693 TYR 0.024 0.002 TYR A 647 ARG 0.004 0.000 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: B 562 HIS cc_start: 0.8239 (m90) cc_final: 0.7951 (m90) REVERT: B 581 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8294 (mt-10) REVERT: B 806 TYR cc_start: 0.8105 (m-10) cc_final: 0.7838 (m-10) REVERT: A 530 ASN cc_start: 0.6733 (t0) cc_final: 0.6371 (t0) REVERT: A 634 CYS cc_start: 0.7130 (p) cc_final: 0.6375 (p) REVERT: A 788 MET cc_start: 0.8509 (mmp) cc_final: 0.8135 (mmm) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1335 time to fit residues: 13.3977 Evaluate side-chains 59 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 22 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 773 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.138589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.120057 restraints weight = 10774.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.122501 restraints weight = 7498.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.124384 restraints weight = 5683.848| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4249 Z= 0.325 Angle : 0.688 6.209 5839 Z= 0.373 Chirality : 0.042 0.129 667 Planarity : 0.005 0.042 780 Dihedral : 10.599 88.473 724 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % 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: -1.58 (0.33), residues: 610 helix: 0.63 (0.30), residues: 271 sheet: -1.71 (1.14), residues: 26 loop : -2.66 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 601 HIS 0.005 0.002 HIS B 661 PHE 0.020 0.003 PHE A 693 TYR 0.024 0.003 TYR A 647 ARG 0.007 0.001 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: A 530 ASN cc_start: 0.7449 (t0) cc_final: 0.7109 (t0) REVERT: A 634 CYS cc_start: 0.7173 (p) cc_final: 0.6421 (p) REVERT: A 788 MET cc_start: 0.8545 (mmp) cc_final: 0.8261 (mmp) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1317 time to fit residues: 12.4478 Evaluate side-chains 58 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 43 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 773 ASN B 790 GLN A 609 ASN A 633 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.143180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.123968 restraints weight = 10418.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.126760 restraints weight = 7071.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.128846 restraints weight = 5246.921| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4249 Z= 0.218 Angle : 0.599 6.022 5839 Z= 0.320 Chirality : 0.040 0.147 667 Planarity : 0.005 0.048 780 Dihedral : 10.200 83.135 724 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 0.35 % Allowed : 1.77 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.34), residues: 610 helix: 0.93 (0.31), residues: 270 sheet: -1.91 (1.06), residues: 27 loop : -2.48 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 752 HIS 0.004 0.001 HIS B 661 PHE 0.024 0.003 PHE A 693 TYR 0.025 0.002 TYR A 647 ARG 0.007 0.000 ARG A 770 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: B 581 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8472 (mt-10) REVERT: B 731 PHE cc_start: 0.8029 (t80) cc_final: 0.7367 (t80) REVERT: A 530 ASN cc_start: 0.7460 (t0) cc_final: 0.7077 (t0) REVERT: A 788 MET cc_start: 0.8604 (mmp) cc_final: 0.8343 (mmm) outliers start: 1 outliers final: 0 residues processed: 71 average time/residue: 0.1397 time to fit residues: 13.2112 Evaluate side-chains 59 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 10 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 773 ASN A 757 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.142202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.123739 restraints weight = 10363.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.126202 restraints weight = 7334.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.127985 restraints weight = 5605.636| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4249 Z= 0.222 Angle : 0.599 6.185 5839 Z= 0.320 Chirality : 0.040 0.142 667 Planarity : 0.005 0.045 780 Dihedral : 9.900 75.127 724 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.34), residues: 610 helix: 1.07 (0.31), residues: 272 sheet: -2.05 (0.83), residues: 40 loop : -2.69 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 601 HIS 0.004 0.001 HIS A 491 PHE 0.020 0.003 PHE A 693 TYR 0.024 0.002 TYR B 582 ARG 0.004 0.000 ARG B 604 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.528 Fit side-chains REVERT: B 581 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8463 (mt-10) REVERT: B 781 LEU cc_start: 0.8783 (tp) cc_final: 0.8572 (mm) REVERT: A 530 ASN cc_start: 0.7485 (t0) cc_final: 0.7083 (t0) REVERT: A 788 MET cc_start: 0.8612 (mmp) cc_final: 0.8287 (mmp) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1374 time to fit residues: 12.4749 Evaluate side-chains 59 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 19 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 633 ASN A 757 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.140768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.122165 restraints weight = 10411.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.124810 restraints weight = 7100.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.126723 restraints weight = 5282.661| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4249 Z= 0.259 Angle : 0.628 6.164 5839 Z= 0.341 Chirality : 0.041 0.141 667 Planarity : 0.005 0.045 780 Dihedral : 9.770 70.030 724 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % 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: -1.23 (0.34), residues: 610 helix: 1.02 (0.31), residues: 270 sheet: -1.58 (1.13), residues: 26 loop : -2.55 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 601 HIS 0.005 0.002 HIS A 708 PHE 0.021 0.003 PHE A 693 TYR 0.034 0.002 TYR A 605 ARG 0.003 0.000 ARG B 604 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: B 731 PHE cc_start: 0.7946 (t80) cc_final: 0.7229 (t80) REVERT: A 530 ASN cc_start: 0.7583 (t0) cc_final: 0.7157 (t0) REVERT: A 788 MET cc_start: 0.8622 (mmp) cc_final: 0.8362 (mmp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1171 time to fit residues: 11.6240 Evaluate side-chains 59 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 27 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 13 optimal weight: 0.2980 chunk 42 optimal weight: 0.0060 chunk 50 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 ASN A 757 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.144297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.125382 restraints weight = 10237.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.128012 restraints weight = 7030.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.129958 restraints weight = 5261.423| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4249 Z= 0.176 Angle : 0.593 6.059 5839 Z= 0.318 Chirality : 0.040 0.150 667 Planarity : 0.005 0.045 780 Dihedral : 9.257 65.185 724 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.35 % Allowed : 1.42 % Favored : 98.23 % 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: -1.01 (0.35), residues: 610 helix: 1.41 (0.32), residues: 269 sheet: -2.37 (0.73), residues: 50 loop : -2.51 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 752 HIS 0.003 0.001 HIS A 626 PHE 0.014 0.002 PHE B 640 TYR 0.025 0.002 TYR B 582 ARG 0.004 0.000 ARG B 604 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 530 ASN cc_start: 0.7318 (t0) cc_final: 0.6913 (t0) REVERT: A 788 MET cc_start: 0.8560 (mmp) cc_final: 0.8195 (mmm) outliers start: 1 outliers final: 0 residues processed: 71 average time/residue: 0.1180 time to fit residues: 11.5059 Evaluate side-chains 57 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 13 optimal weight: 0.8980 chunk 51 optimal weight: 0.1980 chunk 34 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 43 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 ASN A 757 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.145438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.126655 restraints weight = 10243.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.129333 restraints weight = 7084.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.131301 restraints weight = 5299.046| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4249 Z= 0.173 Angle : 0.595 6.390 5839 Z= 0.317 Chirality : 0.039 0.150 667 Planarity : 0.005 0.045 780 Dihedral : 8.940 60.726 724 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.35 % Allowed : 0.35 % Favored : 99.29 % 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: -0.93 (0.35), residues: 610 helix: 1.46 (0.32), residues: 271 sheet: -2.38 (0.71), residues: 52 loop : -2.46 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 752 HIS 0.003 0.001 HIS A 661 PHE 0.016 0.002 PHE B 731 TYR 0.042 0.002 TYR A 605 ARG 0.004 0.000 ARG B 604 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.509 Fit side-chains REVERT: A 530 ASN cc_start: 0.7271 (t0) cc_final: 0.6857 (t0) REVERT: A 788 MET cc_start: 0.8536 (mmp) cc_final: 0.8298 (mmm) outliers start: 1 outliers final: 0 residues processed: 71 average time/residue: 0.1215 time to fit residues: 11.7678 Evaluate side-chains 55 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 12 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 51 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 27 optimal weight: 0.9980 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 633 ASN A 757 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.145702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.126753 restraints weight = 10249.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.129327 restraints weight = 7150.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.131263 restraints weight = 5384.791| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4249 Z= 0.177 Angle : 0.593 6.207 5839 Z= 0.317 Chirality : 0.040 0.147 667 Planarity : 0.005 0.045 780 Dihedral : 8.693 58.565 724 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.35 % Allowed : 0.35 % Favored : 99.29 % 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: -0.90 (0.35), residues: 610 helix: 1.50 (0.32), residues: 268 sheet: -2.28 (0.71), residues: 52 loop : -2.43 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP A 752 HIS 0.003 0.001 HIS A 626 PHE 0.015 0.002 PHE B 731 TYR 0.013 0.002 TYR A 605 ARG 0.004 0.000 ARG B 604 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1471.34 seconds wall clock time: 27 minutes 49.30 seconds (1669.30 seconds total)