Starting phenix.real_space_refine on Thu Mar 5 02:40:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nak_24272/03_2026/7nak_24272_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nak_24272/03_2026/7nak_24272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nak_24272/03_2026/7nak_24272.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nak_24272/03_2026/7nak_24272.map" model { file = "/net/cci-nas-00/data/ceres_data/7nak_24272/03_2026/7nak_24272_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nak_24272/03_2026/7nak_24272_trim.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.075 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: 7 Type Number sf(0) Gaussians I 8 10.91 5 P 16 5.49 5 S 48 5.16 5 C 5976 2.51 5 N 1544 2.21 5 O 1744 1.98 5 H 8967 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18303 Number of models: 1 Model: "" Number of chains: 16 Chain: "D" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2243 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "C" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2242 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "G" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2241 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "B" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2243 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "A" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2242 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "E" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2241 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "F" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2242 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "H" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2241 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'1QD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'1QD': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'1QD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'1QD': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'1QD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'1QD': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'1QD': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'1QD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.41, per 1000 atoms: 0.19 Number of scatterers: 18303 At special positions: 0 Unit cell: (81.45, 80.364, 157.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) I 8 52.95 S 48 16.00 P 16 15.00 O 1744 8.00 N 1544 7.00 C 5976 6.00 H 8967 1.00 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: 1.64 Conformation dependent library (CDL) restraints added in 448.4 milliseconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 9 sheets defined 50.5% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'D' and resid 573 through 587 removed outlier: 3.681A pdb=" N HIS D 587 " --> pdb=" O HIS D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 598 Processing helix chain 'D' and resid 603 through 613 removed outlier: 3.502A pdb=" N LEU D 607 " --> pdb=" O PHE D 603 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE D 608 " --> pdb=" O GLU D 604 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN D 609 " --> pdb=" O ASP D 605 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY D 613 " --> pdb=" O GLN D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 630 removed outlier: 4.425A pdb=" N LYS D 628 " --> pdb=" O ALA D 625 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N MET D 630 " --> pdb=" O ASP D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 650 removed outlier: 3.555A pdb=" N THR D 645 " --> pdb=" O LYS D 641 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA D 646 " --> pdb=" O GLU D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 678 removed outlier: 3.502A pdb=" N GLN D 673 " --> pdb=" O GLU D 670 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ALA D 674 " --> pdb=" O ASP D 671 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE D 678 " --> pdb=" O VAL D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 699 removed outlier: 3.755A pdb=" N GLU D 693 " --> pdb=" O GLU D 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 587 removed outlier: 3.585A pdb=" N ALA C 577 " --> pdb=" O GLY C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 598 Processing helix chain 'C' and resid 603 through 614 removed outlier: 3.524A pdb=" N LEU C 607 " --> pdb=" O PHE C 603 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN C 609 " --> pdb=" O ASP C 605 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C 613 " --> pdb=" O GLN C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 650 removed outlier: 3.568A pdb=" N GLU C 642 " --> pdb=" O TRP C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 668 Processing helix chain 'C' and resid 673 through 678 Processing helix chain 'C' and resid 687 through 699 Processing helix chain 'G' and resid 573 through 585 Processing helix chain 'G' and resid 586 through 588 No H-bonds generated for 'chain 'G' and resid 586 through 588' Processing helix chain 'G' and resid 593 through 598 Processing helix chain 'G' and resid 603 through 614 removed outlier: 4.039A pdb=" N MET G 612 " --> pdb=" O ILE G 608 " (cutoff:3.500A) Processing helix chain 'G' and resid 637 through 649 removed outlier: 3.542A pdb=" N ILE G 643 " --> pdb=" O VAL G 639 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR G 645 " --> pdb=" O LYS G 641 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS G 649 " --> pdb=" O THR G 645 " (cutoff:3.500A) Processing helix chain 'G' and resid 672 through 676 Processing helix chain 'G' and resid 687 through 699 Processing helix chain 'B' and resid 573 through 586 Processing helix chain 'B' and resid 593 through 598 removed outlier: 3.562A pdb=" N LEU B 598 " --> pdb=" O ASP B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 614 removed outlier: 3.755A pdb=" N LYS B 606 " --> pdb=" O LYS B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 649 removed outlier: 3.638A pdb=" N THR B 645 " --> pdb=" O LYS B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 668 Processing helix chain 'B' and resid 669 through 678 removed outlier: 3.677A pdb=" N GLN B 673 " --> pdb=" O GLU B 670 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ALA B 674 " --> pdb=" O ASP B 671 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL B 675 " --> pdb=" O MET B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 699 Processing helix chain 'A' and resid 573 through 587 removed outlier: 3.600A pdb=" N LEU A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS A 587 " --> pdb=" O HIS A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 598 Processing helix chain 'A' and resid 602 through 612 removed outlier: 4.044A pdb=" N LYS A 606 " --> pdb=" O LYS A 602 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE A 608 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 630 Processing helix chain 'A' and resid 637 through 650 removed outlier: 3.620A pdb=" N THR A 645 " --> pdb=" O LYS A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 removed outlier: 3.627A pdb=" N LEU A 676 " --> pdb=" O GLN A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 699 removed outlier: 3.550A pdb=" N GLU A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 587 removed outlier: 4.718A pdb=" N LEU E 576 " --> pdb=" O SER E 572 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS E 587 " --> pdb=" O HIS E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 593 through 598 Processing helix chain 'E' and resid 603 through 614 removed outlier: 3.849A pdb=" N LEU E 607 " --> pdb=" O PHE E 603 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE E 608 " --> pdb=" O GLU E 604 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN E 609 " --> pdb=" O ASP E 605 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N MET E 612 " --> pdb=" O ILE E 608 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY E 613 " --> pdb=" O GLN E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 637 through 649 removed outlier: 3.553A pdb=" N GLU E 642 " --> pdb=" O TRP E 638 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR E 645 " --> pdb=" O LYS E 641 " (cutoff:3.500A) Processing helix chain 'E' and resid 664 through 668 Processing helix chain 'E' and resid 672 through 676 Processing helix chain 'E' and resid 687 through 699 Processing helix chain 'F' and resid 573 through 587 removed outlier: 3.557A pdb=" N VAL F 582 " --> pdb=" O SER F 578 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N HIS F 583 " --> pdb=" O LEU F 579 " (cutoff:3.500A) Processing helix chain 'F' and resid 593 through 598 removed outlier: 3.587A pdb=" N LEU F 598 " --> pdb=" O ASP F 594 " (cutoff:3.500A) Processing helix chain 'F' and resid 602 through 614 removed outlier: 4.055A pdb=" N LYS F 606 " --> pdb=" O LYS F 602 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE F 608 " --> pdb=" O GLU F 604 " (cutoff:3.500A) Processing helix chain 'F' and resid 637 through 649 removed outlier: 3.679A pdb=" N CYS F 649 " --> pdb=" O THR F 645 " (cutoff:3.500A) Processing helix chain 'F' and resid 670 through 678 removed outlier: 4.078A pdb=" N ALA F 674 " --> pdb=" O ASP F 671 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR F 677 " --> pdb=" O ALA F 674 " (cutoff:3.500A) Processing helix chain 'F' and resid 687 through 699 removed outlier: 3.559A pdb=" N GLU F 693 " --> pdb=" O GLU F 689 " (cutoff:3.500A) Processing helix chain 'H' and resid 573 through 586 removed outlier: 3.775A pdb=" N HIS H 583 " --> pdb=" O LEU H 579 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU H 584 " --> pdb=" O LEU H 580 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN H 585 " --> pdb=" O LYS H 581 " (cutoff:3.500A) Processing helix chain 'H' and resid 593 through 597 Processing helix chain 'H' and resid 603 through 612 removed outlier: 4.165A pdb=" N GLN H 609 " --> pdb=" O ASP H 605 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL H 611 " --> pdb=" O LEU H 607 " (cutoff:3.500A) Processing helix chain 'H' and resid 626 through 630 removed outlier: 4.135A pdb=" N MET H 630 " --> pdb=" O ASP H 627 " (cutoff:3.500A) Processing helix chain 'H' and resid 637 through 649 removed outlier: 3.660A pdb=" N ILE H 643 " --> pdb=" O VAL H 639 " (cutoff:3.500A) Processing helix chain 'H' and resid 669 through 678 removed outlier: 4.726A pdb=" N ALA H 674 " --> pdb=" O ASP H 671 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL H 675 " --> pdb=" O MET H 672 " (cutoff:3.500A) Processing helix chain 'H' and resid 687 through 699 Processing sheet with id=AA1, first strand: chain 'D' and resid 591 through 592 removed outlier: 4.060A pdb=" N PHE D 565 " --> pdb=" O ASN D 616 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 591 through 592 removed outlier: 3.649A pdb=" N LEU C 619 " --> pdb=" O VAL C 654 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE C 681 " --> pdb=" O ILE C 653 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 591 through 592 removed outlier: 6.244A pdb=" N PHE G 565 " --> pdb=" O VAL G 618 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL G 620 " --> pdb=" O PHE G 565 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N SER G 567 " --> pdb=" O VAL G 620 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU G 619 " --> pdb=" O VAL G 654 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 591 through 592 removed outlier: 5.883A pdb=" N PHE B 565 " --> pdb=" O VAL B 618 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL B 620 " --> pdb=" O PHE B 565 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N SER B 567 " --> pdb=" O VAL B 620 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE B 617 " --> pdb=" O VAL B 654 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE B 656 " --> pdb=" O PHE B 617 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B 619 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 591 through 592 removed outlier: 5.932A pdb=" N PHE A 565 " --> pdb=" O VAL A 618 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL A 620 " --> pdb=" O PHE A 565 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N SER A 567 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ILE A 681 " --> pdb=" O ILE A 653 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 591 through 592 removed outlier: 6.932A pdb=" N VAL E 564 " --> pdb=" O PHE E 592 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N PHE E 565 " --> pdb=" O VAL E 618 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL E 620 " --> pdb=" O PHE E 565 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N SER E 567 " --> pdb=" O VAL E 620 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU E 619 " --> pdb=" O VAL E 654 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 591 through 592 removed outlier: 6.618A pdb=" N VAL F 564 " --> pdb=" O PHE F 592 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU F 619 " --> pdb=" O VAL F 654 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ILE F 681 " --> pdb=" O ILE F 653 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 591 through 592 removed outlier: 6.804A pdb=" N VAL H 564 " --> pdb=" O PHE H 592 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N PHE H 565 " --> pdb=" O VAL H 618 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL H 620 " --> pdb=" O PHE H 565 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N SER H 567 " --> pdb=" O VAL H 620 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 591 through 592 removed outlier: 6.804A pdb=" N VAL H 564 " --> pdb=" O PHE H 592 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N PHE H 565 " --> pdb=" O VAL H 618 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL H 620 " --> pdb=" O PHE H 565 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N SER H 567 " --> pdb=" O VAL H 620 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE H 656 " --> pdb=" O LEU H 619 " (cutoff:3.500A) 356 hydrogen bonds defined for protein. 936 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.42 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 2.40: 18550 2.40 - 3.96: 0 3.96 - 5.52: 0 5.52 - 7.08: 0 7.08 - 8.64: 1 Warning: very large bond lengths. Bond restraints: 18551 Sorted by residual: bond pdb=" OH TYR H 687 " pdb=" HH TYR H 687 " ideal model delta sigma weight residual 0.840 8.641 -7.801 2.00e-02 2.50e+03 1.52e+05 bond pdb=" C26 1QD E 801 " pdb=" N27 1QD E 801 " ideal model delta sigma weight residual 1.334 1.459 -0.125 2.00e-02 2.50e+03 3.93e+01 bond pdb=" C26 1QD A 801 " pdb=" N27 1QD A 801 " ideal model delta sigma weight residual 1.334 1.459 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" C26 1QD H 801 " pdb=" N27 1QD H 801 " ideal model delta sigma weight residual 1.334 1.459 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" C26 1QD G 801 " pdb=" N27 1QD G 801 " ideal model delta sigma weight residual 1.334 1.458 -0.124 2.00e-02 2.50e+03 3.82e+01 ... (remaining 18546 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 33304 3.36 - 6.71: 205 6.71 - 10.07: 16 10.07 - 13.43: 15 13.43 - 16.78: 10 Bond angle restraints: 33550 Sorted by residual: angle pdb=" O08 1QD B 801 " pdb=" P09 1QD B 801 " pdb=" O11 1QD B 801 " ideal model delta sigma weight residual 93.31 110.09 -16.78 3.00e+00 1.11e-01 3.13e+01 angle pdb=" O08 1QD H 801 " pdb=" P09 1QD H 801 " pdb=" O11 1QD H 801 " ideal model delta sigma weight residual 93.31 109.87 -16.56 3.00e+00 1.11e-01 3.05e+01 angle pdb=" O08 1QD A 801 " pdb=" P09 1QD A 801 " pdb=" O11 1QD A 801 " ideal model delta sigma weight residual 93.31 109.84 -16.53 3.00e+00 1.11e-01 3.04e+01 angle pdb=" O08 1QD D 801 " pdb=" P09 1QD D 801 " pdb=" O11 1QD D 801 " ideal model delta sigma weight residual 93.31 109.33 -16.02 3.00e+00 1.11e-01 2.85e+01 angle pdb=" O08 1QD E 801 " pdb=" P09 1QD E 801 " pdb=" O11 1QD E 801 " ideal model delta sigma weight residual 93.31 109.32 -16.01 3.00e+00 1.11e-01 2.85e+01 ... (remaining 33545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.04: 8512 34.04 - 68.08: 366 68.08 - 102.12: 53 102.12 - 136.16: 10 136.16 - 170.20: 2 Dihedral angle restraints: 8943 sinusoidal: 5048 harmonic: 3895 Sorted by residual: dihedral pdb=" C14 1QD F 801 " pdb=" C12 1QD F 801 " pdb=" C13 1QD F 801 " pdb=" O11 1QD F 801 " ideal model delta sinusoidal sigma weight residual 179.65 -10.15 -170.20 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C12 1QD B 801 " pdb=" O11 1QD B 801 " pdb=" P09 1QD B 801 " pdb=" O30 1QD B 801 " ideal model delta sinusoidal sigma weight residual 85.52 -55.37 140.89 1 3.00e+01 1.11e-03 1.89e+01 dihedral pdb=" C12 1QD B 801 " pdb=" O11 1QD B 801 " pdb=" P09 1QD B 801 " pdb=" O08 1QD B 801 " ideal model delta sinusoidal sigma weight residual 197.89 64.52 133.37 1 3.00e+01 1.11e-03 1.80e+01 ... (remaining 8940 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1212 0.062 - 0.123: 201 0.123 - 0.185: 18 0.185 - 0.246: 10 0.246 - 0.308: 7 Chirality restraints: 1448 Sorted by residual: chirality pdb=" C01 1QD H 801 " pdb=" C02 1QD H 801 " pdb=" N36 1QD H 801 " pdb=" O33 1QD H 801 " both_signs ideal model delta sigma weight residual False 2.38 2.69 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C01 1QD D 801 " pdb=" C02 1QD D 801 " pdb=" N36 1QD D 801 " pdb=" O33 1QD D 801 " both_signs ideal model delta sigma weight residual False 2.38 2.68 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C01 1QD F 801 " pdb=" C02 1QD F 801 " pdb=" N36 1QD F 801 " pdb=" O33 1QD F 801 " both_signs ideal model delta sigma weight residual False 2.38 2.68 -0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 1445 not shown) Planarity restraints: 2664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN H 688 " -0.196 2.00e-02 2.50e+03 2.23e-01 7.44e+02 pdb=" CD GLN H 688 " 0.017 2.00e-02 2.50e+03 pdb=" OE1 GLN H 688 " 0.192 2.00e-02 2.50e+03 pdb=" NE2 GLN H 688 " -0.006 2.00e-02 2.50e+03 pdb="HE21 GLN H 688 " 0.329 2.00e-02 2.50e+03 pdb="HE22 GLN H 688 " -0.337 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN H 609 " 0.190 2.00e-02 2.50e+03 2.15e-01 6.94e+02 pdb=" CD GLN H 609 " -0.017 2.00e-02 2.50e+03 pdb=" OE1 GLN H 609 " -0.186 2.00e-02 2.50e+03 pdb=" NE2 GLN H 609 " 0.007 2.00e-02 2.50e+03 pdb="HE21 GLN H 609 " -0.318 2.00e-02 2.50e+03 pdb="HE22 GLN H 609 " 0.324 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 616 " -0.120 2.00e-02 2.50e+03 1.27e-01 2.42e+02 pdb=" CG ASN G 616 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN G 616 " 0.112 2.00e-02 2.50e+03 pdb=" ND2 ASN G 616 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN G 616 " 0.181 2.00e-02 2.50e+03 pdb="HD22 ASN G 616 " -0.191 2.00e-02 2.50e+03 ... (remaining 2661 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.27: 2920 2.27 - 2.95: 46068 2.95 - 3.62: 56830 3.62 - 4.29: 88167 4.29 - 4.96: 139690 Nonbonded interactions: 333675 Sorted by model distance: nonbonded pdb=" O SER F 574 " pdb=" HG SER F 578 " model vdw 1.602 2.450 nonbonded pdb=" HH TYR C 687 " pdb=" O LYS B 682 " model vdw 1.603 2.450 nonbonded pdb=" O SER E 574 " pdb=" HG SER E 578 " model vdw 1.608 2.450 nonbonded pdb="HH21 ARG H 569 " pdb=" O ALA H 625 " model vdw 1.625 2.450 nonbonded pdb=" HZ1 LYS D 581 " pdb=" OE1 GLN D 585 " model vdw 1.631 2.450 ... (remaining 333670 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 561 through 586 or (resid 587 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or r \ esid 588 through 801)) selection = (chain 'B' and (resid 561 through 586 or (resid 587 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or r \ esid 588 through 639 or (resid 640 and (name N or name CA or name C or name O or \ name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or \ name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid \ 641 through 801)) selection = (chain 'C' and (resid 561 through 586 or (resid 587 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or r \ esid 588 through 639 or (resid 640 and (name N or name CA or name C or name O or \ name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or \ name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid \ 641 through 801)) selection = (chain 'D' and (resid 561 through 586 or (resid 587 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or r \ esid 588 through 639 or (resid 640 and (name N or name CA or name C or name O or \ name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or \ name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid \ 641 through 801)) selection = (chain 'E' and (resid 561 through 586 or (resid 587 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or r \ esid 588 through 801)) selection = (chain 'F' and (resid 561 through 586 or (resid 587 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or r \ esid 588 through 801)) selection = (chain 'G' and (resid 561 through 586 or (resid 587 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or r \ esid 588 through 801)) selection = (chain 'H' and (resid 561 through 586 or (resid 587 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or r \ esid 588 through 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 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: 0.070 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.710 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:7.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 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 : 0.012 0.897 9585 Z= 1.017 Angle : 1.032 16.783 13040 Z= 0.455 Chirality : 0.052 0.308 1448 Planarity : 0.003 0.036 1600 Dihedral : 19.829 170.196 3840 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.26), residues: 1104 helix: -0.98 (0.25), residues: 392 sheet: -0.36 (0.42), residues: 152 loop : 0.01 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 697 TYR 0.009 0.001 TYR B 687 PHE 0.016 0.001 PHE B 660 TRP 0.036 0.002 TRP D 638 HIS 0.006 0.001 HIS B 583 Details of bonding type rmsd covalent geometry : bond 0.00841 ( 9584) covalent geometry : angle 1.03227 (13040) hydrogen bonds : bond 0.31246 ( 356) hydrogen bonds : angle 9.25944 ( 936) Misc. bond : bond 0.89655 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 664 GLU cc_start: 0.7160 (tm-30) cc_final: 0.6612 (tm-30) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 1.2239 time to fit residues: 253.5569 Evaluate side-chains 156 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 587 HIS G 616 ASN B 673 GLN B 688 GLN H 575 GLN H 688 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.211273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.180669 restraints weight = 17123.929| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 1.25 r_work: 0.4111 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.4019 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9585 Z= 0.142 Angle : 0.584 5.321 13040 Z= 0.299 Chirality : 0.043 0.153 1448 Planarity : 0.004 0.052 1600 Dihedral : 17.601 170.029 1624 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.10 % Allowed : 11.20 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.25), residues: 1104 helix: 0.16 (0.25), residues: 408 sheet: -0.46 (0.40), residues: 152 loop : -0.01 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 615 TYR 0.012 0.002 TYR H 687 PHE 0.012 0.001 PHE D 617 TRP 0.017 0.002 TRP D 638 HIS 0.007 0.001 HIS C 587 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9584) covalent geometry : angle 0.58442 (13040) hydrogen bonds : bond 0.05972 ( 356) hydrogen bonds : angle 5.66835 ( 936) Misc. bond : bond 0.00123 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 596 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6517 (tt0) REVERT: G 621 LEU cc_start: 0.7275 (mt) cc_final: 0.7027 (OUTLIER) outliers start: 11 outliers final: 6 residues processed: 169 average time/residue: 1.2437 time to fit residues: 224.0378 Evaluate side-chains 163 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 157 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain G residue 596 GLU Chi-restraints excluded: chain G residue 676 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain F residue 622 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 105 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 76 optimal weight: 0.3980 chunk 17 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.209646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.178455 restraints weight = 18007.716| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 1.32 r_work: 0.4095 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.4000 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9585 Z= 0.142 Angle : 0.552 5.264 13040 Z= 0.281 Chirality : 0.042 0.150 1448 Planarity : 0.004 0.054 1600 Dihedral : 15.816 169.214 1624 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.10 % Allowed : 13.90 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.25), residues: 1104 helix: 0.63 (0.25), residues: 416 sheet: -0.59 (0.39), residues: 152 loop : -0.09 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 615 TYR 0.012 0.002 TYR B 687 PHE 0.013 0.001 PHE B 660 TRP 0.019 0.002 TRP D 638 HIS 0.005 0.001 HIS C 583 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9584) covalent geometry : angle 0.55152 (13040) hydrogen bonds : bond 0.04959 ( 356) hydrogen bonds : angle 5.17607 ( 936) Misc. bond : bond 0.00119 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 172 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 630 MET cc_start: 0.5650 (mpt) cc_final: 0.5437 (mpt) REVERT: D 689 GLU cc_start: 0.7398 (pm20) cc_final: 0.7069 (pm20) REVERT: G 596 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6514 (tt0) REVERT: G 622 SER cc_start: 0.7810 (p) cc_final: 0.7610 (p) outliers start: 11 outliers final: 5 residues processed: 177 average time/residue: 1.2563 time to fit residues: 237.2366 Evaluate side-chains 165 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 159 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain G residue 596 GLU Chi-restraints excluded: chain G residue 676 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain F residue 622 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 28 optimal weight: 1.9990 chunk 90 optimal weight: 0.4980 chunk 95 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 571 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.210063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.178473 restraints weight = 17944.266| |-----------------------------------------------------------------------------| r_work (start): 0.4168 rms_B_bonded: 1.34 r_work: 0.4100 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.4006 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9585 Z= 0.134 Angle : 0.537 4.656 13040 Z= 0.273 Chirality : 0.042 0.148 1448 Planarity : 0.004 0.061 1600 Dihedral : 15.086 171.380 1624 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.40 % Allowed : 15.40 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.26), residues: 1104 helix: 0.77 (0.25), residues: 432 sheet: -0.62 (0.39), residues: 152 loop : 0.00 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 615 TYR 0.012 0.002 TYR H 687 PHE 0.021 0.001 PHE E 603 TRP 0.019 0.002 TRP D 638 HIS 0.005 0.001 HIS C 583 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9584) covalent geometry : angle 0.53745 (13040) hydrogen bonds : bond 0.04259 ( 356) hydrogen bonds : angle 4.91090 ( 936) Misc. bond : bond 0.00080 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 686 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6286 (mp0) REVERT: D 689 GLU cc_start: 0.7493 (pm20) cc_final: 0.7105 (pm20) REVERT: G 621 LEU cc_start: 0.7159 (mt) cc_final: 0.6919 (mp) outliers start: 14 outliers final: 7 residues processed: 171 average time/residue: 1.1893 time to fit residues: 217.3322 Evaluate side-chains 166 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 158 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 686 GLU Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain G residue 676 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain F residue 622 SER Chi-restraints excluded: chain H residue 593 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 6 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 80 optimal weight: 0.0670 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 106 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.210830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.179404 restraints weight = 17743.483| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 1.32 r_work: 0.4109 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.4018 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9585 Z= 0.121 Angle : 0.521 5.606 13040 Z= 0.265 Chirality : 0.041 0.143 1448 Planarity : 0.004 0.072 1600 Dihedral : 14.690 175.474 1624 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.40 % Allowed : 17.10 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.26), residues: 1104 helix: 0.97 (0.26), residues: 432 sheet: -0.58 (0.40), residues: 152 loop : 0.10 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 615 TYR 0.011 0.002 TYR B 687 PHE 0.011 0.001 PHE E 603 TRP 0.019 0.002 TRP D 638 HIS 0.004 0.001 HIS C 583 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9584) covalent geometry : angle 0.52149 (13040) hydrogen bonds : bond 0.03878 ( 356) hydrogen bonds : angle 4.70690 ( 936) Misc. bond : bond 0.00065 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 689 GLU cc_start: 0.7512 (pm20) cc_final: 0.7085 (pm20) REVERT: G 596 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6578 (tt0) REVERT: F 612 MET cc_start: 0.7644 (mmm) cc_final: 0.7109 (mpm) outliers start: 14 outliers final: 8 residues processed: 173 average time/residue: 1.2248 time to fit residues: 225.9913 Evaluate side-chains 169 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 160 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain G residue 596 GLU Chi-restraints excluded: chain G residue 676 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain F residue 622 SER Chi-restraints excluded: chain H residue 593 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 571 ASN A 616 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.208869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.178944 restraints weight = 18309.186| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 1.42 r_work: 0.4070 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3975 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9585 Z= 0.157 Angle : 0.560 6.173 13040 Z= 0.284 Chirality : 0.042 0.150 1448 Planarity : 0.004 0.084 1600 Dihedral : 14.997 178.362 1624 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.60 % Allowed : 18.20 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.26), residues: 1104 helix: 0.77 (0.25), residues: 432 sheet: -0.71 (0.39), residues: 152 loop : 0.03 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 615 TYR 0.014 0.002 TYR H 687 PHE 0.013 0.002 PHE D 617 TRP 0.021 0.002 TRP D 638 HIS 0.006 0.001 HIS C 583 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 9584) covalent geometry : angle 0.56046 (13040) hydrogen bonds : bond 0.04190 ( 356) hydrogen bonds : angle 4.76681 ( 936) Misc. bond : bond 0.00058 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 686 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6327 (mp0) REVERT: D 689 GLU cc_start: 0.7462 (pm20) cc_final: 0.7073 (pm20) REVERT: G 596 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6629 (tt0) REVERT: B 574 SER cc_start: 0.7683 (OUTLIER) cc_final: 0.7397 (m) REVERT: E 627 ASP cc_start: 0.6948 (m-30) cc_final: 0.6716 (m-30) outliers start: 16 outliers final: 10 residues processed: 171 average time/residue: 1.2352 time to fit residues: 225.2500 Evaluate side-chains 171 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 686 GLU Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain G residue 596 GLU Chi-restraints excluded: chain G residue 676 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain F residue 622 SER Chi-restraints excluded: chain H residue 593 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 2 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.209528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.179933 restraints weight = 18603.539| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 1.41 r_work: 0.4096 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.4003 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9585 Z= 0.130 Angle : 0.537 7.049 13040 Z= 0.273 Chirality : 0.042 0.143 1448 Planarity : 0.004 0.091 1600 Dihedral : 14.718 173.716 1624 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.40 % Allowed : 19.20 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.26), residues: 1104 helix: 0.89 (0.26), residues: 432 sheet: -0.68 (0.39), residues: 152 loop : 0.09 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG E 615 TYR 0.012 0.002 TYR H 687 PHE 0.023 0.001 PHE E 603 TRP 0.020 0.002 TRP D 638 HIS 0.004 0.001 HIS C 583 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9584) covalent geometry : angle 0.53686 (13040) hydrogen bonds : bond 0.03880 ( 356) hydrogen bonds : angle 4.65064 ( 936) Misc. bond : bond 0.00063 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 689 GLU cc_start: 0.7448 (pm20) cc_final: 0.7196 (pm20) REVERT: G 596 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6596 (tt0) REVERT: B 574 SER cc_start: 0.7733 (OUTLIER) cc_final: 0.7480 (m) REVERT: E 627 ASP cc_start: 0.7039 (m-30) cc_final: 0.6810 (m-30) outliers start: 14 outliers final: 9 residues processed: 170 average time/residue: 1.2015 time to fit residues: 218.3792 Evaluate side-chains 171 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain G residue 596 GLU Chi-restraints excluded: chain G residue 676 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain F residue 622 SER Chi-restraints excluded: chain H residue 593 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 42 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.208641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.177081 restraints weight = 18125.120| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 1.33 r_work: 0.4089 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3996 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9585 Z= 0.149 Angle : 0.558 7.709 13040 Z= 0.283 Chirality : 0.042 0.147 1448 Planarity : 0.005 0.100 1600 Dihedral : 14.762 166.975 1624 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.60 % Allowed : 18.80 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.26), residues: 1104 helix: 0.83 (0.25), residues: 432 sheet: -0.74 (0.39), residues: 152 loop : 0.07 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 615 TYR 0.013 0.002 TYR H 687 PHE 0.020 0.001 PHE E 603 TRP 0.023 0.002 TRP D 638 HIS 0.005 0.001 HIS C 583 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 9584) covalent geometry : angle 0.55807 (13040) hydrogen bonds : bond 0.03995 ( 356) hydrogen bonds : angle 4.66589 ( 936) Misc. bond : bond 0.00054 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 630 MET cc_start: 0.5890 (mpt) cc_final: 0.5400 (mpt) REVERT: D 686 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6336 (mp0) REVERT: D 689 GLU cc_start: 0.7461 (pm20) cc_final: 0.7104 (pm20) REVERT: G 596 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6667 (tt0) REVERT: B 574 SER cc_start: 0.7727 (OUTLIER) cc_final: 0.7477 (m) REVERT: A 666 GLN cc_start: 0.8423 (pt0) cc_final: 0.8195 (pt0) REVERT: E 627 ASP cc_start: 0.7167 (m-30) cc_final: 0.6959 (m-30) outliers start: 16 outliers final: 9 residues processed: 172 average time/residue: 1.2052 time to fit residues: 221.5371 Evaluate side-chains 174 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 686 GLU Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain G residue 596 GLU Chi-restraints excluded: chain G residue 676 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain F residue 622 SER Chi-restraints excluded: chain H residue 593 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 666 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.208224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.178960 restraints weight = 18375.330| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 1.38 r_work: 0.4079 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3983 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9585 Z= 0.156 Angle : 0.578 8.480 13040 Z= 0.293 Chirality : 0.042 0.146 1448 Planarity : 0.005 0.105 1600 Dihedral : 14.742 162.139 1624 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.30 % Allowed : 20.10 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.26), residues: 1104 helix: 0.85 (0.26), residues: 432 sheet: -0.75 (0.39), residues: 152 loop : 0.10 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG E 615 TYR 0.013 0.002 TYR H 687 PHE 0.016 0.001 PHE E 603 TRP 0.024 0.002 TRP D 638 HIS 0.004 0.001 HIS C 583 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 9584) covalent geometry : angle 0.57828 (13040) hydrogen bonds : bond 0.04003 ( 356) hydrogen bonds : angle 4.66077 ( 936) Misc. bond : bond 0.00054 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 630 MET cc_start: 0.5907 (mpt) cc_final: 0.5405 (mpt) REVERT: D 686 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6351 (mp0) REVERT: D 689 GLU cc_start: 0.7471 (pm20) cc_final: 0.7231 (pm20) REVERT: G 596 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6658 (tt0) REVERT: B 574 SER cc_start: 0.7744 (OUTLIER) cc_final: 0.7489 (m) outliers start: 13 outliers final: 10 residues processed: 166 average time/residue: 1.2204 time to fit residues: 216.2866 Evaluate side-chains 171 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 686 GLU Chi-restraints excluded: chain G residue 596 GLU Chi-restraints excluded: chain G residue 676 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain F residue 622 SER Chi-restraints excluded: chain H residue 593 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 57 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 666 GLN C 571 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.209235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.178438 restraints weight = 17038.860| |-----------------------------------------------------------------------------| r_work (start): 0.4171 rms_B_bonded: 1.27 r_work: 0.4102 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.4011 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9585 Z= 0.133 Angle : 0.565 9.445 13040 Z= 0.286 Chirality : 0.042 0.141 1448 Planarity : 0.005 0.110 1600 Dihedral : 14.438 157.962 1624 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.30 % Allowed : 20.20 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.26), residues: 1104 helix: 1.01 (0.26), residues: 432 sheet: -0.68 (0.39), residues: 152 loop : 0.17 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG E 615 TYR 0.011 0.002 TYR H 687 PHE 0.016 0.001 PHE E 603 TRP 0.025 0.002 TRP D 638 HIS 0.003 0.001 HIS C 583 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 9584) covalent geometry : angle 0.56525 (13040) hydrogen bonds : bond 0.03719 ( 356) hydrogen bonds : angle 4.54822 ( 936) Misc. bond : bond 0.00059 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 630 MET cc_start: 0.5893 (mpt) cc_final: 0.5390 (mpt) REVERT: D 689 GLU cc_start: 0.7452 (pm20) cc_final: 0.7195 (pm20) REVERT: G 596 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6676 (tt0) REVERT: B 574 SER cc_start: 0.7688 (OUTLIER) cc_final: 0.7444 (m) outliers start: 13 outliers final: 9 residues processed: 169 average time/residue: 1.1926 time to fit residues: 215.5924 Evaluate side-chains 174 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 163 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain G residue 596 GLU Chi-restraints excluded: chain G residue 676 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain F residue 622 SER Chi-restraints excluded: chain H residue 593 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 73 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 571 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.209295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.180152 restraints weight = 17972.343| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 1.37 r_work: 0.4095 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3997 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.218 9585 Z= 0.210 Angle : 0.862 59.181 13040 Z= 0.505 Chirality : 0.043 0.429 1448 Planarity : 0.005 0.110 1600 Dihedral : 14.439 157.958 1624 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.10 % Allowed : 20.70 % Favored : 78.20 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.26), residues: 1104 helix: 1.01 (0.26), residues: 432 sheet: -0.68 (0.39), residues: 152 loop : 0.13 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 615 TYR 0.012 0.002 TYR H 687 PHE 0.014 0.001 PHE E 603 TRP 0.021 0.002 TRP D 638 HIS 0.003 0.001 HIS C 583 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 9584) covalent geometry : angle 0.86163 (13040) hydrogen bonds : bond 0.03742 ( 356) hydrogen bonds : angle 4.54826 ( 936) Misc. bond : bond 0.00050 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6151.65 seconds wall clock time: 105 minutes 8.22 seconds (6308.22 seconds total)