Starting phenix.real_space_refine on Tue Nov 19 04:46:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nak_24272/11_2024/7nak_24272_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nak_24272/11_2024/7nak_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nak_24272/11_2024/7nak_24272.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nak_24272/11_2024/7nak_24272.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nak_24272/11_2024/7nak_24272_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nak_24272/11_2024/7nak_24272_trim.cif" } resolution = 2.9 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= 0.075 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): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 12.61, per 1000 atoms: 0.69 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: 5.51 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 2.10 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: 8.25 Time building geometry restraints manager: 6.52 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 700 or resid 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 700 or resid 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 700 or resid 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 700 or resid 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 700 or resid 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 700 or resid 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 700 or resid 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 700 or resid 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: 8.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 49.290 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:16.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.770 ------------------------------------------------------------------------------- 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 : 0.008 0.125 9584 Z= 0.526 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 : 5.96 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 (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: -0.76 (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 TRP 0.036 0.002 TRP D 638 HIS 0.006 0.001 HIS B 583 PHE 0.016 0.001 PHE B 660 TYR 0.009 0.001 TYR B 687 ARG 0.002 0.000 ARG C 697 *********************** 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 : 1.625 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: 0.7159 (tm-30) cc_final: 0.6612 (tm-30) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 2.7820 time to fit residues: 580.9303 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 : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 0.0980 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 101 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 571 ASN B 673 GLN B 688 GLN H 575 GLN H 688 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9584 Z= 0.212 Angle : 0.583 5.346 13040 Z= 0.299 Chirality : 0.043 0.153 1448 Planarity : 0.004 0.051 1600 Dihedral : 17.616 169.852 1624 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.10 % Allowed : 11.00 % Favored : 87.90 % 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: -0.14 (0.25), residues: 1104 helix: 0.15 (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 TRP 0.017 0.002 TRP D 638 HIS 0.007 0.001 HIS C 587 PHE 0.012 0.001 PHE D 617 TYR 0.011 0.002 TYR E 687 ARG 0.007 0.001 ARG E 615 *********************** 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 : 1.498 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: G 596 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6247 (tt0) outliers start: 11 outliers final: 6 residues processed: 169 average time/residue: 2.6634 time to fit residues: 481.5868 Evaluate side-chains 163 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 156 time to evaluate : 1.513 ------------------------------------------------------------------------------- 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 621 LEU 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 56 optimal weight: 0.0050 chunk 31 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 0.0980 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 0.0980 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 575 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9584 Z= 0.158 Angle : 0.504 4.632 13040 Z= 0.258 Chirality : 0.041 0.139 1448 Planarity : 0.004 0.050 1600 Dihedral : 15.038 169.548 1624 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.10 % Allowed : 13.40 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.39 (0.26), residues: 1104 helix: 0.95 (0.26), residues: 416 sheet: -0.48 (0.39), residues: 152 loop : 0.07 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 638 HIS 0.004 0.001 HIS C 640 PHE 0.007 0.001 PHE B 660 TYR 0.012 0.002 TYR B 687 ARG 0.010 0.001 ARG E 615 *********************** 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 181 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 170 time to evaluate : 1.499 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: D 643 ILE cc_start: 0.6548 (mm) cc_final: 0.6003 (mt) outliers start: 11 outliers final: 5 residues processed: 174 average time/residue: 2.7147 time to fit residues: 504.6545 Evaluate side-chains 160 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 155 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.4980 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 0.0030 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9584 Z= 0.179 Angle : 0.512 4.541 13040 Z= 0.261 Chirality : 0.041 0.143 1448 Planarity : 0.004 0.062 1600 Dihedral : 14.740 170.820 1624 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.10 % Allowed : 15.40 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.50 (0.26), residues: 1104 helix: 1.05 (0.26), residues: 432 sheet: -0.51 (0.39), residues: 152 loop : 0.14 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 638 HIS 0.004 0.001 HIS C 583 PHE 0.010 0.001 PHE B 660 TYR 0.011 0.002 TYR G 687 ARG 0.010 0.000 ARG E 615 *********************** 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 178 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 167 time to evaluate : 1.462 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 outliers start: 11 outliers final: 6 residues processed: 170 average time/residue: 2.6134 time to fit residues: 475.5024 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 : 1.503 ------------------------------------------------------------------------------- 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 676 LEU 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 61 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9584 Z= 0.217 Angle : 0.533 5.062 13040 Z= 0.271 Chirality : 0.042 0.148 1448 Planarity : 0.004 0.070 1600 Dihedral : 14.776 174.501 1624 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.30 % Allowed : 16.50 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.42 (0.26), residues: 1104 helix: 1.00 (0.26), residues: 432 sheet: -0.58 (0.39), residues: 152 loop : 0.08 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 638 HIS 0.005 0.001 HIS C 583 PHE 0.023 0.001 PHE E 603 TYR 0.012 0.002 TYR H 687 ARG 0.012 0.000 ARG E 615 *********************** 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 177 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 1.486 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 686 GLU cc_start: 0.6706 (OUTLIER) cc_final: 0.6111 (mp0) REVERT: F 612 MET cc_start: 0.7604 (mmm) cc_final: 0.7087 (mpm) outliers start: 13 outliers final: 6 residues processed: 168 average time/residue: 2.7302 time to fit residues: 492.0793 Evaluate side-chains 167 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 160 time to evaluate : 1.449 ------------------------------------------------------------------------------- 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 676 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain F residue 622 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 571 ASN ** H 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9584 Z= 0.221 Angle : 0.544 5.884 13040 Z= 0.276 Chirality : 0.042 0.146 1448 Planarity : 0.004 0.082 1600 Dihedral : 14.783 177.887 1624 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.40 % Allowed : 17.50 % Favored : 81.10 % 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: 0.38 (0.26), residues: 1104 helix: 0.94 (0.26), residues: 432 sheet: -0.60 (0.39), residues: 152 loop : 0.08 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 638 HIS 0.004 0.001 HIS C 583 PHE 0.014 0.001 PHE E 603 TYR 0.013 0.002 TYR H 687 ARG 0.014 0.000 ARG E 615 *********************** 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 178 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 1.381 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 686 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.6132 (mp0) REVERT: D 689 GLU cc_start: 0.7317 (pm20) cc_final: 0.7020 (pm20) outliers start: 14 outliers final: 8 residues processed: 167 average time/residue: 2.7357 time to fit residues: 489.2781 Evaluate side-chains 171 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 162 time to evaluate : 1.694 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 673 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9584 Z= 0.212 Angle : 0.545 7.041 13040 Z= 0.276 Chirality : 0.042 0.146 1448 Planarity : 0.005 0.092 1600 Dihedral : 14.636 174.762 1624 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.40 % Allowed : 17.70 % Favored : 80.90 % 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: 0.46 (0.26), residues: 1104 helix: 1.00 (0.26), residues: 432 sheet: -0.58 (0.39), residues: 152 loop : 0.14 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 638 HIS 0.004 0.001 HIS C 583 PHE 0.012 0.001 PHE E 603 TYR 0.012 0.002 TYR H 687 ARG 0.017 0.000 ARG E 615 *********************** 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 187 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 173 time to evaluate : 1.475 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: 0.6701 (OUTLIER) cc_final: 0.6113 (mp0) REVERT: D 689 GLU cc_start: 0.7393 (pm20) cc_final: 0.7017 (pm20) outliers start: 14 outliers final: 10 residues processed: 177 average time/residue: 2.5809 time to fit residues: 489.5183 Evaluate side-chains 176 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 165 time to evaluate : 1.743 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 10 optimal weight: 0.0980 chunk 84 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 103 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: ** H 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9584 Z= 0.203 Angle : 0.548 7.701 13040 Z= 0.277 Chirality : 0.041 0.142 1448 Planarity : 0.005 0.099 1600 Dihedral : 14.474 168.197 1624 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.30 % Allowed : 19.00 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.51 (0.26), residues: 1104 helix: 1.07 (0.26), residues: 432 sheet: -0.57 (0.39), residues: 152 loop : 0.16 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 638 HIS 0.004 0.001 HIS C 583 PHE 0.010 0.001 PHE B 660 TYR 0.011 0.002 TYR H 687 ARG 0.018 0.001 ARG E 615 *********************** 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 177 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 1.497 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: 0.6335 (mpt) cc_final: 0.5961 (mpt) REVERT: D 686 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.6180 (mp0) REVERT: D 689 GLU cc_start: 0.7421 (pm20) cc_final: 0.7015 (pm20) REVERT: B 574 SER cc_start: 0.7676 (OUTLIER) cc_final: 0.7473 (m) outliers start: 13 outliers final: 9 residues processed: 168 average time/residue: 2.6207 time to fit residues: 471.8655 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 : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 686 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 0.0030 chunk 95 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.2799 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: