Starting phenix.real_space_refine on Thu Mar 6 00:32:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bcp_44433/03_2025/9bcp_44433.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bcp_44433/03_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_44433/03_2025/9bcp_44433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bcp_44433/03_2025/9bcp_44433.map" model { file = "/net/cci-nas-00/data/ceres_data/9bcp_44433/03_2025/9bcp_44433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bcp_44433/03_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-5624/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: 3.45, per 1000 atoms: 0.83 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: 1.10 Conformation dependent library (CDL) restraints added in 531.3 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: 0.45 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: 0.92 Time building geometry restraints manager: 1.28 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.530 Find NCS groups from input model: 0.220 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.930 ------------------------------------------------------------------------------- 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 : 0.441 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: 0.1383 time to fit residues: 16.2404 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 : 0.489 ------------------------------------------------------------------------------- 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 = 0.125386 restraints weight = 10394.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.127934 restraints weight = 7294.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.129666 restraints weight = 5547.811| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 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 : 0.455 Fit side-chains revert: symmetry clash REVERT: B 581 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8276 (mt-10) REVERT: A 530 ASN cc_start: 0.6845 (t0) cc_final: 0.6492 (t0) REVERT: A 634 CYS cc_start: 0.7075 (p) cc_final: 0.6517 (p) REVERT: A 788 MET cc_start: 0.8376 (mmp) cc_final: 0.8035 (mmp) outliers start: 2 outliers final: 0 residues processed: 79 average time/residue: 0.1391 time to fit residues: 15.0880 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 : 0.395 ------------------------------------------------------------------------------- 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: 0.6980 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 36 optimal weight: 0.0770 overall best weight: 1.5544 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.139762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.121107 restraints weight = 10373.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.123619 restraints weight = 7213.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.125444 restraints weight = 5461.413| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4249 Z= 0.267 Angle : 0.654 6.288 5839 Z= 0.353 Chirality : 0.042 0.136 667 Planarity : 0.005 0.049 780 Dihedral : 11.025 77.936 724 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 0.00 % Allowed : 10.64 % Favored : 89.36 % 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: -1.73 (0.33), residues: 610 helix: 0.61 (0.30), residues: 268 sheet: -2.27 (1.00), residues: 27 loop : -2.77 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 752 HIS 0.006 0.002 HIS A 661 PHE 0.015 0.002 PHE B 707 TYR 0.025 0.002 TYR B 605 ARG 0.004 0.001 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 74 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.439 Fit side-chains REVERT: B 632 SER cc_start: 0.8803 (m) cc_final: 0.8577 (m) REVERT: A 530 ASN cc_start: 0.7184 (t0) cc_final: 0.6874 (t0) REVERT: A 788 MET cc_start: 0.8553 (mmp) cc_final: 0.8314 (mmm) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1315 time to fit residues: 12.7608 Evaluate side-chains 61 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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: 5.9990 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 0.0970 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 50 optimal weight: 0.1980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 B 790 GLN A 757 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.146923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.127335 restraints weight = 10021.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.130362 restraints weight = 6643.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.132491 restraints weight = 4845.235| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2783 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= 0.178 Angle : 0.574 5.859 5839 Z= 0.308 Chirality : 0.040 0.150 667 Planarity : 0.005 0.044 780 Dihedral : 10.706 82.915 724 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % 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: -1.17 (0.34), residues: 610 helix: 1.06 (0.31), residues: 270 sheet: -2.00 (1.02), residues: 27 loop : -2.46 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 752 HIS 0.004 0.001 HIS B 708 PHE 0.014 0.002 PHE A 707 TYR 0.018 0.002 TYR B 605 ARG 0.004 0.000 ARG B 585 *********************** 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 82 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.521 Fit side-chains REVERT: B 581 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8282 (mt-10) REVERT: B 731 PHE cc_start: 0.7957 (t80) cc_final: 0.7287 (t80) REVERT: A 530 ASN cc_start: 0.7175 (t0) cc_final: 0.6815 (t0) REVERT: A 698 GLN cc_start: 0.6405 (mp10) cc_final: 0.4972 (tm-30) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1587 time to fit residues: 16.8498 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 : 0.546 ------------------------------------------------------------------------------- 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: 3.9990 chunk 60 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.142063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.123429 restraints weight = 10494.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.125975 restraints weight = 7131.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.127876 restraints weight = 5356.650| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2974 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= 0.243 Angle : 0.612 6.150 5839 Z= 0.329 Chirality : 0.040 0.138 667 Planarity : 0.005 0.044 780 Dihedral : 10.491 86.606 724 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 0.35 % Allowed : 4.26 % Favored : 95.39 % 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: -1.22 (0.34), residues: 610 helix: 1.06 (0.31), residues: 272 sheet: -2.49 (0.91), residues: 36 loop : -2.49 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 601 HIS 0.004 0.002 HIS A 626 PHE 0.021 0.003 PHE A 707 TYR 0.024 0.002 TYR B 582 ARG 0.003 0.000 ARG B 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 73 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.552 Fit side-chains REVERT: A 530 ASN cc_start: 0.7255 (t0) cc_final: 0.6939 (t0) REVERT: A 698 GLN cc_start: 0.7204 (mp10) cc_final: 0.5396 (tm-30) outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 0.1397 time to fit residues: 13.5203 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 : 0.539 ------------------------------------------------------------------------------- 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: 0.0170 chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 overall best weight: 1.5222 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.141162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.122255 restraints weight = 10421.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.124895 restraints weight = 7072.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.126860 restraints weight = 5280.633| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4249 Z= 0.255 Angle : 0.628 6.071 5839 Z= 0.340 Chirality : 0.041 0.142 667 Planarity : 0.005 0.045 780 Dihedral : 10.290 80.689 724 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % 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: -1.29 (0.34), residues: 610 helix: 1.00 (0.31), residues: 272 sheet: -2.41 (0.92), residues: 36 loop : -2.54 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP A 752 HIS 0.004 0.002 HIS B 661 PHE 0.022 0.003 PHE B 640 TYR 0.033 0.002 TYR A 605 ARG 0.003 0.000 ARG B 585 *********************** 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 75 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.493 Fit side-chains REVERT: B 731 PHE cc_start: 0.8018 (t80) cc_final: 0.7399 (t80) REVERT: A 530 ASN cc_start: 0.7553 (t0) cc_final: 0.7169 (t0) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1225 time to fit residues: 12.3471 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 : 0.448 ------------------------------------------------------------------------------- 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: 5.9990 chunk 17 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 37 optimal weight: 0.0770 chunk 52 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.145364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.126683 restraints weight = 9988.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.129276 restraints weight = 6982.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.131152 restraints weight = 5276.990| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4249 Z= 0.172 Angle : 0.576 6.095 5839 Z= 0.304 Chirality : 0.040 0.147 667 Planarity : 0.005 0.044 780 Dihedral : 9.867 75.608 724 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % 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: -1.08 (0.35), residues: 610 helix: 1.37 (0.32), residues: 272 sheet: -2.68 (0.71), residues: 52 loop : -2.53 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 752 HIS 0.003 0.001 HIS A 626 PHE 0.013 0.002 PHE B 640 TYR 0.014 0.002 TYR A 605 ARG 0.003 0.000 ARG B 585 *********************** 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 74 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.405 Fit side-chains REVERT: B 585 ARG cc_start: 0.8309 (mmt90) cc_final: 0.8018 (mmt180) REVERT: A 530 ASN cc_start: 0.7187 (t0) cc_final: 0.6834 (t0) REVERT: A 633 ASN cc_start: 0.8379 (t0) cc_final: 0.8164 (t0) REVERT: A 640 PHE cc_start: 0.6189 (m-10) cc_final: 0.5965 (m-80) REVERT: A 788 MET cc_start: 0.8222 (mmt) cc_final: 0.7935 (mmm) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1488 time to fit residues: 14.4927 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 : 0.386 ------------------------------------------------------------------------------- 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: 0.6980 chunk 6 optimal weight: 0.1980 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 36 optimal weight: 0.0980 chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 = 0.3855 r_free = 0.3855 target = 0.146226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.127519 restraints weight = 9938.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.130079 restraints weight = 7010.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.131988 restraints weight = 5338.649| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3488 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= 0.160 Angle : 0.580 7.539 5839 Z= 0.306 Chirality : 0.039 0.148 667 Planarity : 0.005 0.045 780 Dihedral : 9.345 69.352 724 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.35), residues: 610 helix: 1.58 (0.32), residues: 272 sheet: -2.50 (0.71), residues: 52 loop : -2.48 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 752 HIS 0.003 0.001 HIS A 661 PHE 0.015 0.002 PHE B 731 TYR 0.038 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 74 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.452 Fit side-chains REVERT: B 585 ARG cc_start: 0.8262 (mmt90) cc_final: 0.7990 (mmt180) REVERT: B 731 PHE cc_start: 0.7899 (t80) cc_final: 0.7436 (t80) REVERT: A 530 ASN cc_start: 0.7287 (t0) cc_final: 0.6861 (t0) REVERT: A 592 LEU cc_start: 0.3654 (tp) cc_final: 0.3420 (tp) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1480 time to fit residues: 14.2064 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 : 0.458 ------------------------------------------------------------------------------- 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: 8.9990 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 13 optimal weight: 0.2980 chunk 42 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 3 optimal weight: 0.0270 chunk 49 optimal weight: 0.7980 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 790 GLN 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 = 0.3866 r_free = 0.3866 target = 0.146987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.127418 restraints weight = 10207.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.130093 restraints weight = 7055.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.132084 restraints weight = 5330.020| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3638 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= 0.181 Angle : 0.585 6.597 5839 Z= 0.308 Chirality : 0.040 0.151 667 Planarity : 0.005 0.045 780 Dihedral : 9.019 63.750 724 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % 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: -0.82 (0.35), residues: 610 helix: 1.55 (0.31), residues: 272 sheet: -2.36 (0.73), residues: 52 loop : -2.39 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 752 HIS 0.003 0.001 HIS A 626 PHE 0.017 0.002 PHE A 693 TYR 0.016 0.002 TYR A 605 ARG 0.002 0.000 ARG A 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 72 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.503 Fit side-chains REVERT: B 582 TYR cc_start: 0.8968 (t80) cc_final: 0.8716 (t80) REVERT: A 530 ASN cc_start: 0.7165 (t0) cc_final: 0.6793 (t0) REVERT: A 592 LEU cc_start: 0.3735 (tp) cc_final: 0.3474 (tp) outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 0.1425 time to fit residues: 13.3574 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 : 0.495 ------------------------------------------------------------------------------- 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: 0.7980 chunk 51 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.139418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.121037 restraints weight = 10215.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.123490 restraints weight = 7162.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.125259 restraints weight = 5460.339| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 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 : 0.005 0.056 4249 Z= 0.322 Angle : 0.697 6.483 5839 Z= 0.376 Chirality : 0.042 0.136 667 Planarity : 0.005 0.045 780 Dihedral : 9.230 59.426 724 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % Rotamer: Outliers : 0.35 % Allowed : 0.00 % Favored : 99.65 % 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: -1.19 (0.34), residues: 610 helix: 1.03 (0.31), residues: 271 sheet: -2.36 (0.93), residues: 38 loop : -2.42 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 601 HIS 0.005 0.002 HIS A 626 PHE 0.018 0.003 PHE B 640 TYR 0.036 0.003 TYR A 605 ARG 0.005 0.001 ARG A 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 69 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.486 Fit side-chains REVERT: B 731 PHE cc_start: 0.8015 (t80) cc_final: 0.7237 (t80) REVERT: A 530 ASN cc_start: 0.7683 (t0) cc_final: 0.7303 (t0) REVERT: A 788 MET cc_start: 0.8356 (mmt) cc_final: 0.8125 (mmt) outliers start: 1 outliers final: 1 residues processed: 69 average time/residue: 0.1241 time to fit residues: 11.5535 Evaluate side-chains 56 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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: 2.9990 chunk 17 optimal weight: 0.0020 chunk 55 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 32 optimal weight: 0.0020 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 633 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.142294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.123047 restraints weight = 10311.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.125653 restraints weight = 7153.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.127565 restraints weight = 5419.218| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4249 Z= 0.200 Angle : 0.612 6.434 5839 Z= 0.326 Chirality : 0.040 0.147 667 Planarity : 0.005 0.046 780 Dihedral : 8.902 61.038 724 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % 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: -0.92 (0.35), residues: 610 helix: 1.32 (0.32), residues: 271 sheet: -2.29 (0.91), residues: 38 loop : -2.34 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 752 HIS 0.003 0.001 HIS A 626 PHE 0.016 0.002 PHE B 603 TYR 0.011 0.002 TYR B 605 ARG 0.003 0.000 ARG B 585 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1516.46 seconds wall clock time: 27 minutes 13.55 seconds (1633.55 seconds total)