Starting phenix.real_space_refine on Fri Dec 27 10:42:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bcp_44433/12_2024/9bcp_44433.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bcp_44433/12_2024/9bcp_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_44433/12_2024/9bcp_44433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bcp_44433/12_2024/9bcp_44433.map" model { file = "/net/cci-nas-00/data/ceres_data/9bcp_44433/12_2024/9bcp_44433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bcp_44433/12_2024/9bcp_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-5532/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: 3.72, per 1000 atoms: 0.89 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: 1.21 Conformation dependent library (CDL) restraints added in 618.2 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: 0.38 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: 0.96 Time building geometry restraints manager: 1.35 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: 1.150 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.840 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.330 ------------------------------------------------------------------------------- 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 : 0.520 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: 0.1420 time to fit residues: 16.5407 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 : 0.439 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 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 : 0.464 Fit side-chains revert: symmetry clash REVERT: B 581 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8154 (mt-10) REVERT: A 530 ASN cc_start: 0.6889 (t0) cc_final: 0.6522 (t0) REVERT: A 634 CYS cc_start: 0.6960 (p) cc_final: 0.6388 (p) REVERT: A 788 MET cc_start: 0.8373 (mmp) cc_final: 0.8026 (mmp) outliers start: 2 outliers final: 0 residues processed: 79 average time/residue: 0.1241 time to fit residues: 13.3554 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 : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 55 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 757 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4249 Z= 0.193 Angle : 0.590 6.057 5839 Z= 0.317 Chirality : 0.040 0.143 667 Planarity : 0.005 0.049 780 Dihedral : 10.837 75.730 724 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % 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: -1.39 (0.34), residues: 610 helix: 0.92 (0.31), residues: 270 sheet: -2.11 (1.02), residues: 27 loop : -2.63 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 752 HIS 0.006 0.001 HIS B 708 PHE 0.010 0.002 PHE A 640 TYR 0.023 0.002 TYR B 605 ARG 0.003 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 75 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.489 Fit side-chains REVERT: B 632 SER cc_start: 0.8652 (m) cc_final: 0.8330 (m) REVERT: A 530 ASN cc_start: 0.6662 (t0) cc_final: 0.6293 (t0) REVERT: A 634 CYS cc_start: 0.6870 (p) cc_final: 0.6247 (p) REVERT: A 788 MET cc_start: 0.8417 (mmp) cc_final: 0.8127 (mmm) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1322 time to fit residues: 13.3560 Evaluate side-chains 63 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 633 ASN B 773 ASN A 757 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4249 Z= 0.248 Angle : 0.617 6.131 5839 Z= 0.332 Chirality : 0.041 0.141 667 Planarity : 0.005 0.046 780 Dihedral : 10.762 84.534 724 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 0.35 % Allowed : 5.32 % Favored : 94.33 % 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: -1.47 (0.33), residues: 610 helix: 0.76 (0.31), residues: 270 sheet: -2.08 (1.01), residues: 27 loop : -2.59 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 601 HIS 0.006 0.002 HIS A 708 PHE 0.022 0.002 PHE A 693 TYR 0.018 0.002 TYR B 605 ARG 0.009 0.001 ARG A 770 *********************** 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 81 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: B 581 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8246 (mt-10) REVERT: B 731 PHE cc_start: 0.7895 (t80) cc_final: 0.7182 (t80) REVERT: A 530 ASN cc_start: 0.7395 (t0) cc_final: 0.7035 (t0) REVERT: A 634 CYS cc_start: 0.6945 (p) cc_final: 0.6274 (p) REVERT: A 788 MET cc_start: 0.8540 (mmp) cc_final: 0.8243 (mmp) outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.1534 time to fit residues: 16.0437 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 : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.3980 chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 0.0470 chunk 52 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 633 ASN B 773 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4249 Z= 0.188 Angle : 0.574 6.656 5839 Z= 0.304 Chirality : 0.040 0.146 667 Planarity : 0.005 0.044 780 Dihedral : 10.447 88.428 724 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.18 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: -1.11 (0.34), residues: 610 helix: 1.16 (0.32), residues: 270 sheet: -2.49 (0.88), residues: 37 loop : -2.41 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 601 HIS 0.004 0.001 HIS B 708 PHE 0.016 0.002 PHE A 693 TYR 0.023 0.002 TYR B 582 ARG 0.002 0.000 ARG A 770 *********************** 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 79 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 530 ASN cc_start: 0.7277 (t0) cc_final: 0.6911 (t0) REVERT: A 634 CYS cc_start: 0.7043 (p) cc_final: 0.6259 (p) REVERT: A 788 MET cc_start: 0.8483 (mmp) cc_final: 0.8214 (mmm) outliers start: 1 outliers final: 0 residues processed: 78 average time/residue: 0.1561 time to fit residues: 15.6044 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 : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 48 optimal weight: 0.0670 chunk 27 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.0270 chunk 30 optimal weight: 1.9990 chunk 56 optimal weight: 0.0170 chunk 6 optimal weight: 5.9990 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 633 ASN B 773 ASN A 633 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3168 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= 0.154 Angle : 0.557 6.133 5839 Z= 0.296 Chirality : 0.039 0.148 667 Planarity : 0.005 0.044 780 Dihedral : 10.036 82.412 724 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.35 % Allowed : 3.19 % 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: -0.96 (0.35), residues: 610 helix: 1.39 (0.32), residues: 272 sheet: -2.48 (0.71), residues: 53 loop : -2.41 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 752 HIS 0.003 0.001 HIS B 708 PHE 0.011 0.001 PHE A 693 TYR 0.036 0.002 TYR A 605 ARG 0.004 0.000 ARG B 604 *********************** 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 72 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: B 581 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8086 (mt-10) REVERT: B 731 PHE cc_start: 0.7764 (t80) cc_final: 0.7207 (t80) REVERT: A 530 ASN cc_start: 0.7278 (t0) cc_final: 0.6895 (t0) REVERT: A 788 MET cc_start: 0.8411 (mmp) cc_final: 0.8184 (mmm) outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 0.1161 time to fit residues: 11.4504 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 : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 773 ASN A 633 ASN A 757 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 4249 Z= 0.345 Angle : 0.680 6.261 5839 Z= 0.368 Chirality : 0.042 0.143 667 Planarity : 0.005 0.044 780 Dihedral : 10.263 75.681 724 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 0.35 % Allowed : 4.96 % 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: -1.23 (0.34), residues: 610 helix: 1.02 (0.31), residues: 270 sheet: -2.07 (0.99), residues: 36 loop : -2.50 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 601 HIS 0.006 0.002 HIS B 661 PHE 0.035 0.004 PHE A 693 TYR 0.017 0.003 TYR A 605 ARG 0.006 0.001 ARG A 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 72 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.500 Fit side-chains REVERT: B 581 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8411 (mt-10) REVERT: A 530 ASN cc_start: 0.7432 (t0) cc_final: 0.7097 (t0) REVERT: A 788 MET cc_start: 0.8611 (mmp) cc_final: 0.8319 (mmp) outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 0.1165 time to fit residues: 11.5800 Evaluate side-chains 54 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 53 optimal weight: 0.0670 chunk 56 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 633 ASN B 790 GLN A 633 ASN A 757 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4249 Z= 0.194 Angle : 0.598 5.967 5839 Z= 0.318 Chirality : 0.040 0.149 667 Planarity : 0.005 0.045 780 Dihedral : 9.865 71.771 724 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.35 % Allowed : 2.48 % 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: -0.93 (0.35), residues: 610 helix: 1.33 (0.32), residues: 270 sheet: -1.93 (0.98), residues: 36 loop : -2.39 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 752 HIS 0.004 0.001 HIS A 708 PHE 0.017 0.002 PHE A 731 TYR 0.038 0.002 TYR A 605 ARG 0.003 0.000 ARG B 585 *********************** 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 77 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: B 581 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8322 (mt-10) REVERT: B 731 PHE cc_start: 0.7729 (t80) cc_final: 0.7220 (t80) REVERT: A 530 ASN cc_start: 0.7569 (t0) cc_final: 0.7094 (t0) REVERT: A 788 MET cc_start: 0.8562 (mmp) cc_final: 0.8274 (mmp) outliers start: 1 outliers final: 0 residues processed: 77 average time/residue: 0.1322 time to fit residues: 13.6130 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 : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.0980 chunk 43 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 40 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4249 Z= 0.175 Angle : 0.586 7.597 5839 Z= 0.308 Chirality : 0.039 0.147 667 Planarity : 0.005 0.045 780 Dihedral : 9.279 64.811 724 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % 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: -0.77 (0.35), residues: 610 helix: 1.58 (0.32), residues: 270 sheet: -1.89 (0.84), residues: 42 loop : -2.44 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A 752 HIS 0.003 0.001 HIS A 661 PHE 0.017 0.002 PHE A 707 TYR 0.020 0.002 TYR A 605 ARG 0.003 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 73 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.504 Fit side-chains REVERT: B 581 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8249 (mt-10) REVERT: A 530 ASN cc_start: 0.7331 (t0) cc_final: 0.6955 (t0) REVERT: A 788 MET cc_start: 0.8522 (mmp) cc_final: 0.8244 (mmm) outliers start: 1 outliers final: 0 residues processed: 73 average time/residue: 0.1187 time to fit residues: 11.9511 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 : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 4.9990 chunk 48 optimal weight: 0.0010 chunk 5 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.8788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4249 Z= 0.187 Angle : 0.594 6.710 5839 Z= 0.313 Chirality : 0.039 0.145 667 Planarity : 0.005 0.046 780 Dihedral : 8.965 59.201 724 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.35 % Allowed : 0.71 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.35), residues: 610 helix: 1.60 (0.32), residues: 270 sheet: -1.82 (0.85), residues: 42 loop : -2.40 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 752 HIS 0.003 0.001 HIS A 626 PHE 0.015 0.002 PHE A 693 TYR 0.041 0.002 TYR A 605 ARG 0.003 0.000 ARG B 585 ********************** 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 72 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: B 581 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8268 (mt-10) REVERT: B 585 ARG cc_start: 0.8205 (mmt90) cc_final: 0.7982 (mmt90) REVERT: A 530 ASN cc_start: 0.7378 (t0) cc_final: 0.6967 (t0) REVERT: A 788 MET cc_start: 0.8582 (mmp) cc_final: 0.8229 (mmm) outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 0.1348 time to fit residues: 13.2641 Evaluate side-chains 56 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 0.0970 chunk 2 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 757 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.143352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.124024 restraints weight = 10275.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.126634 restraints weight = 7103.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.128622 restraints weight = 5358.114| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4249 Z= 0.215 Angle : 0.602 6.656 5839 Z= 0.318 Chirality : 0.040 0.141 667 Planarity : 0.005 0.045 780 Dihedral : 8.791 59.899 724 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % 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: -0.83 (0.35), residues: 610 helix: 1.56 (0.32), residues: 270 sheet: -2.20 (0.79), residues: 50 loop : -2.43 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 601 HIS 0.004 0.001 HIS A 708 PHE 0.030 0.002 PHE A 693 TYR 0.018 0.002 TYR A 605 ARG 0.002 0.000 ARG A 604 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1165.80 seconds wall clock time: 21 minutes 58.52 seconds (1318.52 seconds total)