Starting phenix.real_space_refine on Sun Apr 5 03:32:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rw4_54298/04_2026/9rw4_54298.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rw4_54298/04_2026/9rw4_54298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rw4_54298/04_2026/9rw4_54298.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rw4_54298/04_2026/9rw4_54298.map" model { file = "/net/cci-nas-00/data/ceres_data/9rw4_54298/04_2026/9rw4_54298.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rw4_54298/04_2026/9rw4_54298.cif" } resolution = 3.9 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= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 84 5.49 5 S 12 5.16 5 C 4491 2.51 5 N 1433 2.21 5 O 1761 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7781 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 334 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'TRANS': 52} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 7, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 79 Chain: "B" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 334 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'TRANS': 52} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 7, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 79 Chain: "D" Number of atoms: 2670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 2670 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 271} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 436} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 967 Unresolved non-hydrogen angles: 1219 Unresolved non-hydrogen dihedrals: 792 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'ASP:plan': 17, 'TRP:plan': 2, 'GLN:plan1': 20, 'ASN:plan1': 14, 'PHE:plan': 8, 'TYR:plan': 11, 'GLU:plan': 20, 'ARG:plan': 15, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 491 Chain: "C" Number of atoms: 2635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 2635 Classifications: {'peptide': 449} Incomplete info: {'truncation_to_alanine': 285} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 438} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1024 Unresolved non-hydrogen angles: 1288 Unresolved non-hydrogen dihedrals: 839 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLU:plan': 23, 'ASP:plan': 21, 'HIS:plan': 5, 'ARG:plan': 16, 'GLN:plan1': 21, 'TRP:plan': 2, 'ASN:plan1': 14, 'PHE:plan': 8, 'TYR:plan': 11} Unresolved non-hydrogen planarities: 529 Chain: "E" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 904 Classifications: {'RNA': 43} Modifications used: {'5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 19, 'rna3p_pyr': 22} Link IDs: {'rna2p': 2, 'rna3p': 40} Chain breaks: 1 Chain: "F" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 904 Classifications: {'RNA': 43} Modifications used: {'5*END': 1, 'rna2p_pyr': 3, 'rna3p_pur': 19, 'rna3p_pyr': 21} Link IDs: {'rna2p': 3, 'rna3p': 39} Chain breaks: 1 Time building chain proxies: 1.95, per 1000 atoms: 0.25 Number of scatterers: 7781 At special positions: 0 Unit cell: (84.8, 109.18, 169.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 84 15.00 O 1761 8.00 N 1433 7.00 C 4491 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 308.7 milliseconds 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1916 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 10 sheets defined 71.0% alpha, 5.9% beta 35 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 695 through 747 removed outlier: 3.842A pdb=" N VAL A 699 " --> pdb=" O CYS A 695 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 747 Processing helix chain 'D' and resid 6 through 25 removed outlier: 3.899A pdb=" N LYS D 24 " --> pdb=" O ARG D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 37 Processing helix chain 'D' and resid 43 through 50 Processing helix chain 'D' and resid 53 through 63 Processing helix chain 'D' and resid 96 through 111 removed outlier: 3.775A pdb=" N PHE D 104 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR D 111 " --> pdb=" O LYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 125 removed outlier: 3.702A pdb=" N GLY D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N HIS D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 128 No H-bonds generated for 'chain 'D' and resid 126 through 128' Processing helix chain 'D' and resid 130 through 137 removed outlier: 3.687A pdb=" N SER D 137 " --> pdb=" O VAL D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 152 removed outlier: 3.592A pdb=" N PHE D 147 " --> pdb=" O GLU D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 529 Processing helix chain 'D' and resid 535 through 554 Processing helix chain 'D' and resid 590 through 592 No H-bonds generated for 'chain 'D' and resid 590 through 592' Processing helix chain 'D' and resid 593 through 600 removed outlier: 4.138A pdb=" N VAL D 597 " --> pdb=" O CYS D 593 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR D 598 " --> pdb=" O PRO D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 608 removed outlier: 3.556A pdb=" N VAL D 605 " --> pdb=" O GLY D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 629 removed outlier: 4.508A pdb=" N ASP D 621 " --> pdb=" O ASP D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 639 through 652 Processing helix chain 'D' and resid 654 through 658 Processing helix chain 'D' and resid 662 through 671 Processing helix chain 'D' and resid 676 through 688 removed outlier: 3.602A pdb=" N GLN D 680 " --> pdb=" O PRO D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 694 Processing helix chain 'D' and resid 698 through 714 removed outlier: 4.317A pdb=" N ASP D 708 " --> pdb=" O TYR D 704 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL D 709 " --> pdb=" O ALA D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 723 removed outlier: 3.509A pdb=" N ASN D 720 " --> pdb=" O GLN D 716 " (cutoff:3.500A) Processing helix chain 'D' and resid 726 through 742 Processing helix chain 'D' and resid 746 through 773 removed outlier: 3.864A pdb=" N SER D 764 " --> pdb=" O SER D 760 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP D 765 " --> pdb=" O THR D 761 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU D 766 " --> pdb=" O GLU D 762 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS D 767 " --> pdb=" O VAL D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 780 through 787 Processing helix chain 'D' and resid 788 through 790 No H-bonds generated for 'chain 'D' and resid 788 through 790' Processing helix chain 'D' and resid 793 through 801 Processing helix chain 'D' and resid 803 through 816 Processing helix chain 'C' and resid 6 through 25 Processing helix chain 'C' and resid 30 through 36 Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 53 through 63 removed outlier: 3.670A pdb=" N GLN C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 111 removed outlier: 4.166A pdb=" N GLU C 99 " --> pdb=" O ASP C 95 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET C 108 " --> pdb=" O PHE C 104 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN C 110 " --> pdb=" O ASN C 106 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 127 Processing helix chain 'C' and resid 130 through 137 removed outlier: 3.569A pdb=" N ILE C 136 " --> pdb=" O GLN C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 152 Processing helix chain 'C' and resid 521 through 530 Processing helix chain 'C' and resid 535 through 554 removed outlier: 3.595A pdb=" N ASN C 553 " --> pdb=" O TYR C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 600 Processing helix chain 'C' and resid 601 through 608 removed outlier: 3.503A pdb=" N VAL C 605 " --> pdb=" O GLY C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 630 removed outlier: 3.531A pdb=" N ALA C 623 " --> pdb=" O ARG C 619 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN C 624 " --> pdb=" O ASN C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 639 through 652 Processing helix chain 'C' and resid 654 through 658 Processing helix chain 'C' and resid 662 through 670 Processing helix chain 'C' and resid 675 through 688 removed outlier: 4.078A pdb=" N ASP C 679 " --> pdb=" O ASN C 675 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN C 680 " --> pdb=" O PRO C 676 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN C 683 " --> pdb=" O ASP C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 694 removed outlier: 3.843A pdb=" N TRP C 692 " --> pdb=" O GLN C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 714 removed outlier: 3.704A pdb=" N ASP C 708 " --> pdb=" O TYR C 704 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL C 709 " --> pdb=" O ALA C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 723 Processing helix chain 'C' and resid 726 through 742 Processing helix chain 'C' and resid 746 through 772 Processing helix chain 'C' and resid 780 through 786 Processing helix chain 'C' and resid 793 through 802 Processing helix chain 'C' and resid 803 through 816 removed outlier: 3.839A pdb=" N LYS C 808 " --> pdb=" O TYR C 804 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU C 814 " --> pdb=" O LEU C 810 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 28 through 29 Processing sheet with id=AA2, first strand: chain 'D' and resid 155 through 158 removed outlier: 3.603A pdb=" N MET D 163 " --> pdb=" O LYS D 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 530 through 533 removed outlier: 7.195A pdb=" N THR D 531 " --> pdb=" O LEU D 587 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 577 through 579 removed outlier: 5.712A pdb=" N ILE D 556 " --> pdb=" O ILE D 612 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL D 614 " --> pdb=" O ILE D 556 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL D 558 " --> pdb=" O VAL D 614 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 564 through 565 Processing sheet with id=AA6, first strand: chain 'C' and resid 28 through 29 removed outlier: 3.563A pdb=" N ARG C 28 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN C 76 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 155 through 158 Processing sheet with id=AA8, first strand: chain 'C' and resid 531 through 533 Processing sheet with id=AA9, first strand: chain 'C' and resid 556 through 559 removed outlier: 6.195A pdb=" N ILE C 556 " --> pdb=" O ILE C 612 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL C 614 " --> pdb=" O ILE C 556 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL C 558 " --> pdb=" O VAL C 614 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N PHE C 637 " --> pdb=" O VAL C 611 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LYS C 613 " --> pdb=" O PHE C 637 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 564 through 565 removed outlier: 3.655A pdb=" N GLU C 572 " --> pdb=" O ILE C 565 " (cutoff:3.500A) 488 hydrogen bonds defined for protein. 1404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 84 hydrogen bonds 160 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 1.41 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2428 1.34 - 1.46: 1511 1.46 - 1.58: 3908 1.58 - 1.70: 166 1.70 - 1.82: 20 Bond restraints: 8033 Sorted by residual: bond pdb=" N CYS A 695 " pdb=" CA CYS A 695 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" N CYS B 695 " pdb=" CA CYS B 695 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.86e+00 bond pdb=" CG ARG D 120 " pdb=" CD ARG D 120 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.04e+00 bond pdb=" CB LYS C 40 " pdb=" CG LYS C 40 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.75e+00 bond pdb=" CB LYS D 156 " pdb=" CG LYS D 156 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.46e+00 ... (remaining 8028 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 11166 1.65 - 3.30: 184 3.30 - 4.95: 34 4.95 - 6.60: 4 6.60 - 8.25: 2 Bond angle restraints: 11390 Sorted by residual: angle pdb=" N ARG D 120 " pdb=" CA ARG D 120 " pdb=" C ARG D 120 " ideal model delta sigma weight residual 111.28 108.15 3.13 1.09e+00 8.42e-01 8.26e+00 angle pdb=" CA LYS D 105 " pdb=" CB LYS D 105 " pdb=" CG LYS D 105 " ideal model delta sigma weight residual 114.10 119.63 -5.53 2.00e+00 2.50e-01 7.64e+00 angle pdb=" C1' U E 39 " pdb=" N1 U E 39 " pdb=" C2 U E 39 " ideal model delta sigma weight residual 117.70 125.95 -8.25 3.00e+00 1.11e-01 7.56e+00 angle pdb=" CB MET C 8 " pdb=" CG MET C 8 " pdb=" SD MET C 8 " ideal model delta sigma weight residual 112.70 120.82 -8.12 3.00e+00 1.11e-01 7.32e+00 angle pdb=" CA LYS D 156 " pdb=" CB LYS D 156 " pdb=" CG LYS D 156 " ideal model delta sigma weight residual 114.10 118.97 -4.87 2.00e+00 2.50e-01 5.94e+00 ... (remaining 11385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.01: 4413 22.01 - 44.03: 292 44.03 - 66.04: 148 66.04 - 88.06: 33 88.06 - 110.07: 6 Dihedral angle restraints: 4892 sinusoidal: 1966 harmonic: 2926 Sorted by residual: dihedral pdb=" O4' U E 39 " pdb=" C1' U E 39 " pdb=" N1 U E 39 " pdb=" C2 U E 39 " ideal model delta sinusoidal sigma weight residual 200.00 122.43 77.57 1 1.50e+01 4.44e-03 3.35e+01 dihedral pdb=" N LEU C 14 " pdb=" CA LEU C 14 " pdb=" CB LEU C 14 " pdb=" CG LEU C 14 " ideal model delta sinusoidal sigma weight residual -60.00 -119.40 59.40 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" O5' U F 35 " pdb=" C5' U F 35 " pdb=" C4' U F 35 " pdb=" C3' U F 35 " ideal model delta sinusoidal sigma weight residual -65.00 -6.95 -58.05 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 4889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 990 0.028 - 0.056: 321 0.056 - 0.083: 94 0.083 - 0.111: 52 0.111 - 0.139: 18 Chirality restraints: 1475 Sorted by residual: chirality pdb=" C1' A F 3 " pdb=" O4' A F 3 " pdb=" C2' A F 3 " pdb=" N9 A F 3 " both_signs ideal model delta sigma weight residual False 2.46 2.32 0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA ILE C 578 " pdb=" N ILE C 578 " pdb=" C ILE C 578 " pdb=" CB ILE C 578 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA ILE C 631 " pdb=" N ILE C 631 " pdb=" C ILE C 631 " pdb=" CB ILE C 631 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.64e-01 ... (remaining 1472 not shown) Planarity restraints: 1222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A F 3 " 0.028 2.00e-02 2.50e+03 1.35e-02 5.00e+00 pdb=" N9 A F 3 " -0.033 2.00e-02 2.50e+03 pdb=" C8 A F 3 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A F 3 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A F 3 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A F 3 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A F 3 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A F 3 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A F 3 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A F 3 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A F 3 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 117 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.35e+00 pdb=" N PRO D 118 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO D 118 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 118 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 120 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.44e+00 pdb=" C ARG D 120 " -0.027 2.00e-02 2.50e+03 pdb=" O ARG D 120 " 0.010 2.00e-02 2.50e+03 pdb=" N SER D 121 " 0.009 2.00e-02 2.50e+03 ... (remaining 1219 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 97 2.60 - 3.18: 7380 3.18 - 3.75: 13318 3.75 - 4.33: 16163 4.33 - 4.90: 24720 Nonbonded interactions: 61678 Sorted by model distance: nonbonded pdb=" O2' C F 38 " pdb=" OP1 U F 40 " model vdw 2.030 3.040 nonbonded pdb=" O PRO C 118 " pdb=" N ARG C 120 " model vdw 2.208 3.120 nonbonded pdb=" O2' C E 38 " pdb=" OP1 U E 40 " model vdw 2.232 3.040 nonbonded pdb=" O THR C 154 " pdb=" N VAL C 165 " model vdw 2.242 3.120 nonbonded pdb=" O2' G F 45 " pdb=" O4' U F 46 " model vdw 2.281 3.040 ... (remaining 61673 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' selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 5 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 81 or resid 95 through 107 or (re \ sid 108 and (name N or name CA or name C or name O or name CB )) or resid 109 th \ rough 816)) selection = (chain 'D' and (resid 5 through 43 or (resid 44 through 45 and (name N or name C \ A or name C or name O or name CB )) or resid 46 through 72 or (resid 73 and (nam \ e N or name CA or name C or name O or name CB )) or resid 74 through 100 or (res \ id 101 and (name N or name CA or name C or name O or name CB )) or resid 102 thr \ ough 115 or (resid 116 and (name N or name CA or name C or name O or name CB )) \ or resid 117 through 119 or (resid 120 and (name N or name CA or name C or name \ O or name CB )) or resid 121 through 138 or (resid 139 and (name N or name CA or \ name C or name O or name CB )) or resid 140 through 141 or (resid 142 through 1 \ 43 and (name N or name CA or name C or name O or name CB )) or resid 144 through \ 145 or (resid 146 and (name N or name CA or name C or name O or name CB )) or r \ esid 147 through 148 or (resid 149 and (name N or name CA or name C or name O or \ name CB )) or resid 150 through 152 or (resid 153 and (name N or name CA or nam \ e C or name O or name CB )) or resid 154 through 155 or (resid 156 and (name N o \ r name CA or name C or name O or name CB )) or resid 157 or (resid 158 through 1 \ 60 and (name N or name CA or name C or name O or name CB )) or resid 161 through \ 816)) } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.390 Find NCS groups from input model: 0.120 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:1.160 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 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 : 0.002 0.043 8033 Z= 0.121 Angle : 0.552 8.250 11390 Z= 0.301 Chirality : 0.035 0.139 1475 Planarity : 0.003 0.046 1222 Dihedral : 19.428 110.074 2976 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.35 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 23.91 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.52 (0.27), residues: 986 helix: 1.14 (0.21), residues: 595 sheet: -1.35 (0.73), residues: 48 loop : -0.72 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 120 TYR 0.012 0.001 TYR D 64 PHE 0.008 0.001 PHE C 68 TRP 0.000 0.000 TRP D 522 HIS 0.006 0.001 HIS C 151 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 8033) covalent geometry : angle 0.55173 (11390) hydrogen bonds : bond 0.22490 ( 572) hydrogen bonds : angle 7.80938 ( 1564) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.251 Fit side-chains REVERT: A 713 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8216 (tm-30) REVERT: A 717 LYS cc_start: 0.9161 (tptt) cc_final: 0.8615 (tppt) REVERT: D 102 ASP cc_start: 0.7789 (m-30) cc_final: 0.7250 (t0) REVERT: D 106 ASN cc_start: 0.8051 (m-40) cc_final: 0.7736 (m110) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1106 time to fit residues: 14.9882 Evaluate side-chains 87 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 40.0000 chunk 33 optimal weight: 50.0000 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 0.0980 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 140 HIS C 54 GLN C 125 HIS C 128 GLN C 151 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.082266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.061301 restraints weight = 38158.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.062313 restraints weight = 26115.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.062919 restraints weight = 20749.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.063349 restraints weight = 18137.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.063433 restraints weight = 16664.887| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 8033 Z= 0.281 Angle : 0.651 8.730 11390 Z= 0.336 Chirality : 0.040 0.149 1475 Planarity : 0.004 0.066 1222 Dihedral : 18.561 107.704 2344 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.35 % Favored : 96.45 % Rotamer: Outliers : 4.71 % Allowed : 17.03 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.30 (0.27), residues: 986 helix: 1.65 (0.20), residues: 651 sheet: -1.57 (0.71), residues: 49 loop : -0.43 (0.40), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 126 TYR 0.011 0.002 TYR D 111 PHE 0.014 0.002 PHE C 60 TRP 0.000 0.000 TRP D 522 HIS 0.007 0.001 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00579 ( 8033) covalent geometry : angle 0.65053 (11390) hydrogen bonds : bond 0.05756 ( 572) hydrogen bonds : angle 5.29701 ( 1564) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 713 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8186 (tm-30) REVERT: A 714 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8170 (mm-30) REVERT: A 717 LYS cc_start: 0.9082 (tptt) cc_final: 0.8688 (tptp) REVERT: C 24 LYS cc_start: 0.8725 (tptt) cc_final: 0.8451 (tptm) outliers start: 13 outliers final: 10 residues processed: 100 average time/residue: 0.1078 time to fit residues: 13.8110 Evaluate side-chains 87 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 165 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 42 optimal weight: 7.9990 chunk 78 optimal weight: 30.0000 chunk 2 optimal weight: 0.9980 chunk 84 optimal weight: 40.0000 chunk 4 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 75 optimal weight: 40.0000 chunk 76 optimal weight: 50.0000 chunk 60 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 729 GLN D 48 GLN ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.084605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.063491 restraints weight = 38680.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.064550 restraints weight = 26860.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.065163 restraints weight = 21381.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.065605 restraints weight = 18660.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.065653 restraints weight = 17181.984| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8033 Z= 0.170 Angle : 0.545 8.505 11390 Z= 0.280 Chirality : 0.037 0.143 1475 Planarity : 0.003 0.049 1222 Dihedral : 18.390 106.897 2344 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.25 % Favored : 96.65 % Rotamer: Outliers : 5.43 % Allowed : 18.48 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.04 (0.28), residues: 986 helix: 2.28 (0.20), residues: 651 sheet: -1.43 (0.73), residues: 50 loop : -0.29 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 120 TYR 0.008 0.001 TYR D 64 PHE 0.011 0.001 PHE D 17 TRP 0.000 0.000 TRP D 522 HIS 0.007 0.001 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8033) covalent geometry : angle 0.54503 (11390) hydrogen bonds : bond 0.04504 ( 572) hydrogen bonds : angle 4.49484 ( 1564) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 713 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8127 (tm-30) REVERT: A 714 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8242 (mm-30) REVERT: A 717 LYS cc_start: 0.9009 (tptt) cc_final: 0.8647 (tptp) REVERT: D 142 LYS cc_start: 0.8592 (ptmt) cc_final: 0.8309 (ptmm) REVERT: C 108 MET cc_start: 0.6963 (ttm) cc_final: 0.6480 (tmm) REVERT: C 151 HIS cc_start: 0.7226 (OUTLIER) cc_final: 0.6709 (m90) outliers start: 15 outliers final: 9 residues processed: 104 average time/residue: 0.0932 time to fit residues: 12.7102 Evaluate side-chains 94 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 3 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 45 optimal weight: 50.0000 chunk 9 optimal weight: 10.0000 chunk 41 optimal weight: 50.0000 chunk 97 optimal weight: 40.0000 chunk 28 optimal weight: 30.0000 chunk 4 optimal weight: 5.9990 chunk 78 optimal weight: 30.0000 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 729 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.082645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.061091 restraints weight = 39232.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.062178 restraints weight = 26921.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.062773 restraints weight = 21197.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.063067 restraints weight = 18489.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.063429 restraints weight = 17203.666| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8033 Z= 0.289 Angle : 0.624 9.367 11390 Z= 0.322 Chirality : 0.039 0.146 1475 Planarity : 0.004 0.053 1222 Dihedral : 18.506 108.020 2344 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.85 % Favored : 96.04 % Rotamer: Outliers : 6.52 % Allowed : 21.74 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.75 (0.27), residues: 986 helix: 2.07 (0.20), residues: 651 sheet: -1.43 (0.72), residues: 49 loop : -0.46 (0.39), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 126 TYR 0.014 0.002 TYR D 64 PHE 0.014 0.002 PHE C 60 TRP 0.000 0.000 TRP D 522 HIS 0.006 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00598 ( 8033) covalent geometry : angle 0.62434 (11390) hydrogen bonds : bond 0.05264 ( 572) hydrogen bonds : angle 4.71016 ( 1564) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.173 Fit side-chains REVERT: A 713 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8162 (tm-30) REVERT: A 714 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8100 (mm-30) REVERT: A 717 LYS cc_start: 0.9003 (tptt) cc_final: 0.8644 (tptp) REVERT: A 721 GLN cc_start: 0.8573 (mt0) cc_final: 0.8049 (mt0) REVERT: B 714 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7548 (mm-30) REVERT: C 151 HIS cc_start: 0.7340 (OUTLIER) cc_final: 0.6700 (m90) outliers start: 18 outliers final: 11 residues processed: 98 average time/residue: 0.0996 time to fit residues: 12.7522 Evaluate side-chains 94 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 165 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 45 optimal weight: 50.0000 chunk 35 optimal weight: 5.9990 chunk 88 optimal weight: 50.0000 chunk 10 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 40 optimal weight: 30.0000 chunk 26 optimal weight: 50.0000 chunk 18 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 729 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.084417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.063415 restraints weight = 39007.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.064419 restraints weight = 27034.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.065112 restraints weight = 21597.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.065289 restraints weight = 18825.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.065582 restraints weight = 17723.148| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8033 Z= 0.161 Angle : 0.534 9.076 11390 Z= 0.275 Chirality : 0.037 0.229 1475 Planarity : 0.003 0.048 1222 Dihedral : 18.338 106.762 2344 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.14 % Favored : 96.65 % Rotamer: Outliers : 4.71 % Allowed : 23.91 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.12 (0.28), residues: 986 helix: 2.40 (0.20), residues: 650 sheet: -1.38 (0.71), residues: 50 loop : -0.41 (0.39), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 126 TYR 0.013 0.001 TYR D 64 PHE 0.012 0.001 PHE D 17 TRP 0.000 0.000 TRP D 522 HIS 0.004 0.001 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8033) covalent geometry : angle 0.53381 (11390) hydrogen bonds : bond 0.04227 ( 572) hydrogen bonds : angle 4.23772 ( 1564) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 713 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8031 (tm-30) REVERT: A 714 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8081 (mm-30) REVERT: D 101 LYS cc_start: 0.8975 (ttpp) cc_final: 0.8726 (ttpp) REVERT: C 151 HIS cc_start: 0.7261 (OUTLIER) cc_final: 0.6606 (m90) outliers start: 13 outliers final: 8 residues processed: 107 average time/residue: 0.0994 time to fit residues: 13.9404 Evaluate side-chains 98 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 45 optimal weight: 50.0000 chunk 9 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 20 optimal weight: 0.5980 chunk 90 optimal weight: 30.0000 chunk 59 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 71 optimal weight: 50.0000 chunk 47 optimal weight: 20.0000 chunk 35 optimal weight: 50.0000 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.083151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.061817 restraints weight = 39169.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.062858 restraints weight = 26492.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.063608 restraints weight = 20872.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.063961 restraints weight = 18075.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.063961 restraints weight = 16723.688| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8033 Z= 0.239 Angle : 0.584 9.510 11390 Z= 0.301 Chirality : 0.038 0.196 1475 Planarity : 0.004 0.056 1222 Dihedral : 18.385 107.738 2344 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.06 % Favored : 95.74 % Rotamer: Outliers : 5.80 % Allowed : 23.19 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.96 (0.28), residues: 986 helix: 2.31 (0.20), residues: 650 sheet: -1.39 (0.70), residues: 50 loop : -0.56 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 47 TYR 0.013 0.001 TYR D 64 PHE 0.011 0.002 PHE C 60 TRP 0.000 0.000 TRP D 522 HIS 0.006 0.001 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00499 ( 8033) covalent geometry : angle 0.58375 (11390) hydrogen bonds : bond 0.04716 ( 572) hydrogen bonds : angle 4.41333 ( 1564) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 713 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8056 (tm-30) REVERT: A 714 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8023 (mm-30) REVERT: D 101 LYS cc_start: 0.8999 (ttpp) cc_final: 0.8790 (ttpp) REVERT: C 126 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8206 (ttt180) REVERT: C 151 HIS cc_start: 0.7282 (OUTLIER) cc_final: 0.6491 (m90) outliers start: 16 outliers final: 12 residues processed: 100 average time/residue: 0.0970 time to fit residues: 12.6275 Evaluate side-chains 98 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 165 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 79 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 86 optimal weight: 40.0000 chunk 48 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 98 optimal weight: 6.9990 chunk 84 optimal weight: 30.0000 chunk 9 optimal weight: 0.7980 chunk 51 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 overall best weight: 5.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.081852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.060393 restraints weight = 39411.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.061369 restraints weight = 26860.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.062111 restraints weight = 21273.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.062578 restraints weight = 18473.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.062719 restraints weight = 16900.683| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 8033 Z= 0.372 Angle : 0.706 10.431 11390 Z= 0.363 Chirality : 0.041 0.155 1475 Planarity : 0.004 0.055 1222 Dihedral : 18.468 108.811 2344 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.46 % Favored : 95.33 % Rotamer: Outliers : 6.88 % Allowed : 23.19 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.53 (0.27), residues: 986 helix: 1.96 (0.20), residues: 649 sheet: -1.51 (0.70), residues: 50 loop : -0.70 (0.39), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 134 TYR 0.013 0.002 TYR D 64 PHE 0.017 0.002 PHE C 60 TRP 0.000 0.000 TRP D 522 HIS 0.007 0.002 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00772 ( 8033) covalent geometry : angle 0.70636 (11390) hydrogen bonds : bond 0.05606 ( 572) hydrogen bonds : angle 4.76868 ( 1564) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.251 Fit side-chains REVERT: A 713 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8123 (tm-30) REVERT: A 714 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8133 (mm-30) REVERT: D 101 LYS cc_start: 0.9044 (ttpp) cc_final: 0.8602 (ttpp) REVERT: C 126 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8220 (ttt180) REVERT: C 151 HIS cc_start: 0.7498 (OUTLIER) cc_final: 0.6816 (m90) outliers start: 19 outliers final: 16 residues processed: 100 average time/residue: 0.0953 time to fit residues: 12.7349 Evaluate side-chains 97 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 165 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 12 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 chunk 39 optimal weight: 30.0000 chunk 103 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 5 optimal weight: 30.0000 chunk 55 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.085039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.064325 restraints weight = 39191.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.065380 restraints weight = 26665.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.066027 restraints weight = 21065.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.066354 restraints weight = 18364.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.066354 restraints weight = 17039.573| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8033 Z= 0.120 Angle : 0.536 9.114 11390 Z= 0.274 Chirality : 0.035 0.152 1475 Planarity : 0.003 0.044 1222 Dihedral : 18.291 106.810 2344 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.55 % Favored : 96.25 % Rotamer: Outliers : 5.07 % Allowed : 26.45 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.21 (0.28), residues: 986 helix: 2.50 (0.20), residues: 652 sheet: -1.40 (0.69), residues: 50 loop : -0.48 (0.40), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 120 TYR 0.013 0.001 TYR D 64 PHE 0.012 0.001 PHE D 17 TRP 0.000 0.000 TRP D 522 HIS 0.004 0.001 HIS D 125 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 8033) covalent geometry : angle 0.53551 (11390) hydrogen bonds : bond 0.03889 ( 572) hydrogen bonds : angle 4.08722 ( 1564) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 713 GLU cc_start: 0.8342 (tm-30) cc_final: 0.8056 (tm-30) REVERT: A 714 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8049 (mm-30) REVERT: B 714 GLU cc_start: 0.7604 (mm-30) cc_final: 0.6327 (mm-30) REVERT: D 143 GLU cc_start: 0.7799 (mp0) cc_final: 0.7511 (mp0) REVERT: D 150 LYS cc_start: 0.8573 (tmtt) cc_final: 0.8089 (ptmm) REVERT: C 151 HIS cc_start: 0.7165 (OUTLIER) cc_final: 0.6411 (m90) outliers start: 14 outliers final: 9 residues processed: 106 average time/residue: 0.0971 time to fit residues: 13.4996 Evaluate side-chains 99 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 99 optimal weight: 7.9990 chunk 52 optimal weight: 40.0000 chunk 75 optimal weight: 50.0000 chunk 83 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 37 optimal weight: 20.0000 chunk 35 optimal weight: 50.0000 chunk 73 optimal weight: 40.0000 chunk 48 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 overall best weight: 7.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.080417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.061654 restraints weight = 39549.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.060424 restraints weight = 37240.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.060956 restraints weight = 31174.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.061517 restraints weight = 24002.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.061439 restraints weight = 21900.827| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.090 8033 Z= 0.492 Angle : 0.853 11.762 11390 Z= 0.440 Chirality : 0.046 0.240 1475 Planarity : 0.006 0.102 1222 Dihedral : 18.754 111.878 2344 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.38 % Favored : 94.42 % Rotamer: Outliers : 5.43 % Allowed : 26.81 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.89 (0.27), residues: 986 helix: 1.47 (0.20), residues: 654 sheet: -1.47 (0.72), residues: 47 loop : -1.06 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 126 TYR 0.021 0.003 TYR D 103 PHE 0.023 0.003 PHE D 60 TRP 0.000 0.000 TRP D 522 HIS 0.008 0.002 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.01021 ( 8033) covalent geometry : angle 0.85282 (11390) hydrogen bonds : bond 0.06622 ( 572) hydrogen bonds : angle 5.27562 ( 1564) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.216 Fit side-chains REVERT: A 713 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8147 (tm-30) REVERT: A 714 GLU cc_start: 0.8675 (mm-30) cc_final: 0.7967 (mm-30) REVERT: B 714 GLU cc_start: 0.7537 (mm-30) cc_final: 0.6819 (mm-30) REVERT: B 717 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8242 (ptpp) REVERT: C 151 HIS cc_start: 0.7523 (OUTLIER) cc_final: 0.6857 (m90) outliers start: 15 outliers final: 13 residues processed: 91 average time/residue: 0.0844 time to fit residues: 10.3294 Evaluate side-chains 92 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 717 LYS Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 165 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 39 optimal weight: 30.0000 chunk 19 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 62 optimal weight: 0.6980 chunk 74 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 36 optimal weight: 50.0000 chunk 30 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.084528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.063638 restraints weight = 38485.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.064831 restraints weight = 24778.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.065597 restraints weight = 19074.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.066032 restraints weight = 16300.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.066098 restraints weight = 14857.259| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8033 Z= 0.127 Angle : 0.587 10.341 11390 Z= 0.302 Chirality : 0.036 0.159 1475 Planarity : 0.004 0.051 1222 Dihedral : 18.356 107.764 2344 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.04 % Favored : 96.75 % Rotamer: Outliers : 3.99 % Allowed : 28.99 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.91 (0.28), residues: 986 helix: 2.24 (0.20), residues: 656 sheet: -1.30 (0.71), residues: 47 loop : -0.61 (0.40), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 126 TYR 0.016 0.001 TYR D 103 PHE 0.015 0.001 PHE D 17 TRP 0.000 0.000 TRP D 522 HIS 0.004 0.001 HIS D 125 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8033) covalent geometry : angle 0.58717 (11390) hydrogen bonds : bond 0.04128 ( 572) hydrogen bonds : angle 4.21243 ( 1564) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 713 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8071 (tm-30) REVERT: A 714 GLU cc_start: 0.8672 (mm-30) cc_final: 0.7985 (mm-30) REVERT: B 714 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6339 (mm-30) REVERT: B 717 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8277 (ptpp) REVERT: D 150 LYS cc_start: 0.8510 (tmtt) cc_final: 0.8136 (ptmm) REVERT: C 24 LYS cc_start: 0.8421 (tppt) cc_final: 0.7590 (tptm) REVERT: C 151 HIS cc_start: 0.7082 (OUTLIER) cc_final: 0.6361 (m90) outliers start: 11 outliers final: 7 residues processed: 101 average time/residue: 0.0988 time to fit residues: 13.0723 Evaluate side-chains 100 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 717 LYS Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 102 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 chunk 39 optimal weight: 40.0000 chunk 80 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 72 optimal weight: 30.0000 chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 50.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.084299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.063279 restraints weight = 39039.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.064468 restraints weight = 25158.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.065239 restraints weight = 19343.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.065636 restraints weight = 16523.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.065705 restraints weight = 15164.256| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8033 Z= 0.150 Angle : 0.573 10.424 11390 Z= 0.293 Chirality : 0.036 0.137 1475 Planarity : 0.004 0.061 1222 Dihedral : 18.233 107.592 2344 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.65 % Favored : 96.15 % Rotamer: Outliers : 3.62 % Allowed : 29.35 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.08 (0.28), residues: 986 helix: 2.36 (0.20), residues: 658 sheet: -1.15 (0.73), residues: 47 loop : -0.55 (0.40), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 126 TYR 0.018 0.001 TYR D 103 PHE 0.012 0.001 PHE D 17 TRP 0.000 0.000 TRP D 522 HIS 0.003 0.001 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8033) covalent geometry : angle 0.57316 (11390) hydrogen bonds : bond 0.04069 ( 572) hydrogen bonds : angle 4.08495 ( 1564) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1275.05 seconds wall clock time: 22 minutes 37.28 seconds (1357.28 seconds total)