Starting phenix.real_space_refine on Thu Jul 2 10:17:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rw2_54296/07_2026/9rw2_54296.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rw2_54296/07_2026/9rw2_54296.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rw2_54296/07_2026/9rw2_54296.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rw2_54296/07_2026/9rw2_54296.map" model { file = "/net/cci-nas-00/data/ceres_data/9rw2_54296/07_2026/9rw2_54296.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rw2_54296/07_2026/9rw2_54296.cif" } resolution = 3.6 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= 0.002 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 88 5.49 5 S 19 5.16 5 C 4693 2.51 5 N 1490 2.21 5 O 1837 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8127 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 365 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'TRANS': 52} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 58 Chain: "B" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 365 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'TRANS': 52} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 58 Chain: "D" Number of atoms: 2780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 2780 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 274} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 450} Chain breaks: 3 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 981 Unresolved non-hydrogen angles: 1242 Unresolved non-hydrogen dihedrals: 801 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLU:plan': 22, 'ASN:plan1': 17, 'TYR:plan': 12, 'ASP:plan': 16, 'TRP:plan': 2, 'GLN:plan1': 20, 'PHE:plan': 8, 'ARG:plan': 15, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 512 Chain: "C" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 2767 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 274} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 448} Chain breaks: 3 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 981 Unresolved non-hydrogen angles: 1242 Unresolved non-hydrogen dihedrals: 801 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLU:plan': 22, 'ASN:plan1': 17, 'TYR:plan': 12, 'ASP:plan': 16, 'TRP:plan': 2, 'GLN:plan1': 20, 'PHE:plan': 8, 'ARG:plan': 15, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 512 Chain: "E" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 925 Classifications: {'RNA': 44} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 21, 'rna3p_pyr': 22} Link IDs: {'rna2p': 1, 'rna3p': 42} Chain: "F" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 925 Classifications: {'RNA': 44} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 21, 'rna3p_pyr': 22} Link IDs: {'rna2p': 1, 'rna3p': 42} Time building chain proxies: 1.57, per 1000 atoms: 0.19 Number of scatterers: 8127 At special positions: 0 Unit cell: (94.251, 95.31, 175.794, 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 19 16.00 P 88 15.00 O 1837 8.00 N 1490 7.00 C 4693 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: 0.71 Conformation dependent library (CDL) restraints added in 300.8 milliseconds 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1964 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 6 sheets defined 68.6% alpha, 5.7% beta 34 base pairs and 54 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 695 through 747 removed outlier: 3.605A pdb=" N VAL A 699 " --> pdb=" O CYS A 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 747 Processing helix chain 'D' and resid 3 through 25 removed outlier: 3.672A pdb=" N LYS D 24 " --> pdb=" O ARG D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 36 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 43 through 50 Processing helix chain 'D' and resid 53 through 63 removed outlier: 3.542A pdb=" N GLN D 63 " --> pdb=" O LYS D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 110 Processing helix chain 'D' and resid 119 through 125 removed outlier: 3.865A pdb=" N HIS D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 129 Processing helix chain 'D' and resid 130 through 138 Processing helix chain 'D' and resid 140 through 151 Processing helix chain 'D' and resid 521 through 530 Processing helix chain 'D' and resid 535 through 554 Processing helix chain 'D' and resid 594 through 600 removed outlier: 3.940A pdb=" N THR D 598 " --> pdb=" O PRO D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 608 Processing helix chain 'D' and resid 617 through 628 removed outlier: 4.540A 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 670 removed outlier: 3.642A pdb=" N TYR D 670 " --> pdb=" O LEU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 676 through 680 Processing helix chain 'D' and resid 681 through 688 removed outlier: 3.817A pdb=" N TYR D 685 " --> pdb=" O LEU D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 714 removed outlier: 3.546A pdb=" N MET D 702 " --> pdb=" O THR D 698 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP D 708 " --> pdb=" O TYR D 704 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL D 709 " --> pdb=" O ALA D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 725 Processing helix chain 'D' and resid 726 through 728 No H-bonds generated for 'chain 'D' and resid 726 through 728' Processing helix chain 'D' and resid 729 through 743 Processing helix chain 'D' and resid 746 through 773 removed outlier: 3.894A pdb=" N THR D 773 " --> pdb=" O LYS D 769 " (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 802 removed outlier: 4.014A pdb=" N GLY D 802 " --> pdb=" O GLU D 798 " (cutoff:3.500A) 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 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 42 through 50 removed outlier: 3.950A pdb=" N MET C 46 " --> pdb=" O PHE C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 62 Processing helix chain 'C' and resid 96 through 110 removed outlier: 3.687A pdb=" N GLN C 110 " --> pdb=" O ASN C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 127 Processing helix chain 'C' and resid 130 through 138 removed outlier: 3.569A pdb=" N GLY C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 150 Processing helix chain 'C' and resid 521 through 530 removed outlier: 3.642A pdb=" N GLN C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN C 529 " --> pdb=" O LYS C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 554 Processing helix chain 'C' and resid 594 through 600 removed outlier: 3.879A pdb=" N THR C 598 " --> pdb=" O PRO C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 608 removed outlier: 3.629A pdb=" N VAL C 605 " --> pdb=" O GLY C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 629 removed outlier: 4.366A pdb=" N ASP C 621 " --> pdb=" O ASP C 617 " (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 removed outlier: 3.625A pdb=" N TYR C 670 " --> pdb=" O LEU C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 680 removed outlier: 3.867A pdb=" N LYS C 678 " --> pdb=" O ASN C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 688 removed outlier: 4.433A pdb=" N TYR C 685 " --> pdb=" O LEU C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 714 removed outlier: 3.695A pdb=" N MET C 702 " --> pdb=" O THR C 698 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP C 708 " --> pdb=" O TYR C 704 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL C 709 " --> pdb=" O ALA C 705 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS C 714 " --> pdb=" O LEU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 724 Processing helix chain 'C' and resid 729 through 743 Processing helix chain 'C' and resid 746 through 773 removed outlier: 4.140A pdb=" N THR C 773 " --> pdb=" O LYS C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 780 through 787 removed outlier: 3.808A pdb=" N ARG C 785 " --> pdb=" O ASN C 781 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 790 No H-bonds generated for 'chain 'C' and resid 788 through 790' Processing helix chain 'C' and resid 793 through 800 Processing helix chain 'C' and resid 803 through 816 removed outlier: 3.653A 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 117 through 118 Processing sheet with id=AA3, first strand: chain 'D' and resid 531 through 533 removed outlier: 3.501A pdb=" N ILE D 576 " --> pdb=" O PHE D 588 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 28 through 29 Processing sheet with id=AA5, first strand: chain 'C' and resid 155 through 158 Processing sheet with id=AA6, first strand: chain 'C' and resid 585 through 588 removed outlier: 3.544A pdb=" N ILE C 578 " --> pdb=" O PHE C 586 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE C 576 " --> pdb=" O PHE C 588 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LYS C 613 " --> pdb=" O PHE C 637 " (cutoff:3.500A) 498 hydrogen bonds defined for protein. 1440 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 54 stacking parallelities Total time for adding SS restraints: 0.98 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1710 1.33 - 1.45: 2184 1.45 - 1.57: 4286 1.57 - 1.69: 174 1.69 - 1.82: 34 Bond restraints: 8388 Sorted by residual: bond pdb=" N1 C F 1 " pdb=" C6 C F 1 " ideal model delta sigma weight residual 1.367 1.383 -0.016 6.00e-03 2.78e+04 7.17e+00 bond pdb=" N1 C F 36 " pdb=" C6 C F 36 " ideal model delta sigma weight residual 1.367 1.381 -0.014 6.00e-03 2.78e+04 5.57e+00 bond pdb=" N9 A F 37 " pdb=" C4 A F 37 " ideal model delta sigma weight residual 1.374 1.387 -0.013 6.00e-03 2.78e+04 5.00e+00 bond pdb=" N1 U F 11 " pdb=" C6 U F 11 " ideal model delta sigma weight residual 1.375 1.395 -0.020 9.00e-03 1.23e+04 4.97e+00 bond pdb=" C5 U F 23 " pdb=" C6 U F 23 " ideal model delta sigma weight residual 1.337 1.356 -0.019 9.00e-03 1.23e+04 4.47e+00 ... (remaining 8383 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 10991 1.18 - 2.36: 716 2.36 - 3.54: 113 3.54 - 4.72: 21 4.72 - 5.90: 8 Bond angle restraints: 11849 Sorted by residual: angle pdb=" N6 A F 37 " pdb=" C6 A F 37 " pdb=" N1 A F 37 " ideal model delta sigma weight residual 118.60 115.03 3.57 6.00e-01 2.78e+00 3.55e+01 angle pdb=" N6 A F 22 " pdb=" C6 A F 22 " pdb=" N1 A F 22 " ideal model delta sigma weight residual 118.60 115.56 3.04 6.00e-01 2.78e+00 2.57e+01 angle pdb=" N6 A F 21 " pdb=" C6 A F 21 " pdb=" N1 A F 21 " ideal model delta sigma weight residual 118.60 115.59 3.01 6.00e-01 2.78e+00 2.51e+01 angle pdb=" C1' U E 11 " pdb=" N1 U E 11 " pdb=" C2 U E 11 " ideal model delta sigma weight residual 117.70 123.60 -5.90 1.20e+00 6.94e-01 2.42e+01 angle pdb=" N6 A F 31 " pdb=" C6 A F 31 " pdb=" N1 A F 31 " ideal model delta sigma weight residual 118.60 115.65 2.95 6.00e-01 2.78e+00 2.42e+01 ... (remaining 11844 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 4865 35.89 - 71.78: 179 71.78 - 107.67: 15 107.67 - 143.57: 0 143.57 - 179.46: 2 Dihedral angle restraints: 5061 sinusoidal: 2063 harmonic: 2998 Sorted by residual: dihedral pdb=" C4' C F 33 " pdb=" C3' C F 33 " pdb=" O3' C F 33 " pdb=" P U F 34 " ideal model delta sinusoidal sigma weight residual 220.00 40.54 179.46 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' C E 33 " pdb=" C3' C E 33 " pdb=" O3' C E 33 " pdb=" P U E 34 " ideal model delta sinusoidal sigma weight residual 220.00 45.91 174.09 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA THR D 574 " pdb=" C THR D 574 " pdb=" N LEU D 575 " pdb=" CA LEU D 575 " ideal model delta harmonic sigma weight residual 180.00 161.66 18.34 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 5058 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1065 0.035 - 0.069: 323 0.069 - 0.104: 87 0.104 - 0.138: 38 0.138 - 0.173: 3 Chirality restraints: 1516 Sorted by residual: chirality pdb=" C3' A F 32 " pdb=" C4' A F 32 " pdb=" O3' A F 32 " pdb=" C2' A F 32 " both_signs ideal model delta sigma weight residual False -2.48 -2.65 0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" C3' C F 33 " pdb=" C4' C F 33 " pdb=" O3' C F 33 " pdb=" C2' C F 33 " both_signs ideal model delta sigma weight residual False -2.48 -2.31 -0.17 2.00e-01 2.50e+01 7.25e-01 chirality pdb=" C3' C F 1 " pdb=" C4' C F 1 " pdb=" O3' C F 1 " pdb=" C2' C F 1 " both_signs ideal model delta sigma weight residual False -2.48 -2.63 0.16 2.00e-01 2.50e+01 6.11e-01 ... (remaining 1513 not shown) Planarity restraints: 1272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A F 21 " -0.051 2.00e-02 2.50e+03 2.17e-02 1.29e+01 pdb=" N9 A F 21 " 0.017 2.00e-02 2.50e+03 pdb=" C8 A F 21 " 0.009 2.00e-02 2.50e+03 pdb=" N7 A F 21 " 0.012 2.00e-02 2.50e+03 pdb=" C5 A F 21 " 0.012 2.00e-02 2.50e+03 pdb=" C6 A F 21 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A F 21 " -0.037 2.00e-02 2.50e+03 pdb=" N1 A F 21 " -0.006 2.00e-02 2.50e+03 pdb=" C2 A F 21 " 0.006 2.00e-02 2.50e+03 pdb=" N3 A F 21 " 0.016 2.00e-02 2.50e+03 pdb=" C4 A F 21 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A F 10 " -0.052 2.00e-02 2.50e+03 2.16e-02 1.28e+01 pdb=" N9 A F 10 " 0.027 2.00e-02 2.50e+03 pdb=" C8 A F 10 " 0.016 2.00e-02 2.50e+03 pdb=" N7 A F 10 " 0.010 2.00e-02 2.50e+03 pdb=" C5 A F 10 " 0.003 2.00e-02 2.50e+03 pdb=" C6 A F 10 " -0.001 2.00e-02 2.50e+03 pdb=" N6 A F 10 " -0.032 2.00e-02 2.50e+03 pdb=" N1 A F 10 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A F 10 " 0.007 2.00e-02 2.50e+03 pdb=" N3 A F 10 " 0.012 2.00e-02 2.50e+03 pdb=" C4 A F 10 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G F 8 " -0.046 2.00e-02 2.50e+03 1.96e-02 1.15e+01 pdb=" N9 G F 8 " 0.019 2.00e-02 2.50e+03 pdb=" C8 G F 8 " 0.025 2.00e-02 2.50e+03 pdb=" N7 G F 8 " 0.016 2.00e-02 2.50e+03 pdb=" C5 G F 8 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G F 8 " -0.011 2.00e-02 2.50e+03 pdb=" O6 G F 8 " -0.021 2.00e-02 2.50e+03 pdb=" N1 G F 8 " -0.007 2.00e-02 2.50e+03 pdb=" C2 G F 8 " -0.005 2.00e-02 2.50e+03 pdb=" N2 G F 8 " 0.024 2.00e-02 2.50e+03 pdb=" N3 G F 8 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G F 8 " 0.004 2.00e-02 2.50e+03 ... (remaining 1269 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 56 2.57 - 3.15: 7026 3.15 - 3.74: 13440 3.74 - 4.32: 16517 4.32 - 4.90: 25564 Nonbonded interactions: 62603 Sorted by model distance: nonbonded pdb=" O2' C E 33 " pdb=" OP1 U E 34 " model vdw 1.990 3.040 nonbonded pdb=" OG1 THR D 43 " pdb=" OE1 GLU D 45 " model vdw 2.005 3.040 nonbonded pdb=" NE2 GLN C 139 " pdb=" OP1 A F 30 " model vdw 2.070 3.120 nonbonded pdb=" O2' C E 36 " pdb=" OP1 A E 38 " model vdw 2.156 3.040 nonbonded pdb=" OG SER C 55 " pdb=" NZ LYS C 59 " model vdw 2.189 3.120 ... (remaining 62598 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 81 or resid 92 through 816)) selection = (chain 'D' and resid 5 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.590 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 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 : 0.003 0.026 8388 Z= 0.261 Angle : 0.652 5.902 11849 Z= 0.599 Chirality : 0.039 0.173 1516 Planarity : 0.004 0.056 1272 Dihedral : 17.557 179.458 3097 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 21.30 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.32 (0.26), residues: 1008 helix: 0.86 (0.20), residues: 609 sheet: -1.78 (0.62), residues: 61 loop : -0.41 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 126 TYR 0.013 0.001 TYR D 6 PHE 0.009 0.001 PHE C 17 TRP 0.000 0.000 TRP D 522 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.26 ( 8388) covalent geometry : angle 0.65197 / 0.60 (11849) hydrogen bonds : bond 0.15592 / 11.02 ( 570) hydrogen bonds : angle 6.50985 / 4.81 ( 1576) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.217 Fit side-chains REVERT: B 714 GLU cc_start: 0.7777 (tp30) cc_final: 0.7503 (tp30) REVERT: B 716 LYS cc_start: 0.8351 (mttt) cc_final: 0.8119 (mttm) REVERT: B 725 LEU cc_start: 0.8371 (mt) cc_final: 0.7632 (tp) REVERT: D 160 ASP cc_start: 0.7684 (t70) cc_final: 0.7453 (t0) REVERT: C 99 GLU cc_start: 0.8471 (tt0) cc_final: 0.7802 (tt0) REVERT: C 102 ASP cc_start: 0.8471 (m-30) cc_final: 0.8122 (p0) REVERT: C 111 TYR cc_start: 0.6881 (m-10) cc_final: 0.6443 (m-10) REVERT: C 126 ARG cc_start: 0.7594 (tmt170) cc_final: 0.6791 (tmm-80) REVERT: C 146 ASP cc_start: 0.8590 (m-30) cc_final: 0.8320 (m-30) REVERT: C 149 MET cc_start: 0.8167 (mtp) cc_final: 0.7936 (ptp) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.0670 time to fit residues: 10.3248 Evaluate side-chains 95 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 30.0000 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 40.0000 chunk 33 optimal weight: 0.0170 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 20.0000 chunk 100 optimal weight: 30.0000 chunk 106 optimal weight: 10.0000 overall best weight: 4.3026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN C 128 GLN C 132 GLN C 139 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 = 0.4006 r_free = 0.4006 target = 0.105542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.084157 restraints weight = 32192.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.083447 restraints weight = 25311.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.084654 restraints weight = 18932.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.085082 restraints weight = 15086.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.085046 restraints weight = 13559.637| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8388 Z= 0.243 Angle : 0.570 7.114 11849 Z= 0.334 Chirality : 0.040 0.206 1516 Planarity : 0.004 0.046 1272 Dihedral : 15.887 163.242 2324 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 6.17 % Allowed : 20.37 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.99 (0.26), residues: 1008 helix: 1.44 (0.20), residues: 648 sheet: -1.68 (0.64), residues: 59 loop : -0.45 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 126 TYR 0.013 0.002 TYR C 64 PHE 0.019 0.003 PHE C 17 TRP 0.000 0.000 TRP D 522 HIS 0.004 0.001 HIS D 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.24 ( 8388) covalent geometry : angle 0.56990 / 0.33 (11849) hydrogen bonds : bond 0.05480 / 3.81 ( 570) hydrogen bonds : angle 4.97918 / 3.76 ( 1576) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: B 716 LYS cc_start: 0.8431 (mttt) cc_final: 0.8024 (mttm) REVERT: D 108 MET cc_start: 0.8427 (mmm) cc_final: 0.8081 (mmm) REVERT: C 99 GLU cc_start: 0.8187 (tt0) cc_final: 0.7629 (tt0) REVERT: C 116 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7539 (mm-30) REVERT: C 123 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.7967 (mm) REVERT: C 126 ARG cc_start: 0.7767 (tmt170) cc_final: 0.6970 (tmm-80) outliers start: 20 outliers final: 12 residues processed: 110 average time/residue: 0.0670 time to fit residues: 10.3727 Evaluate side-chains 98 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 735 GLN Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain C residue 12 MET Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 110 GLN Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 145 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 75 optimal weight: 40.0000 chunk 49 optimal weight: 20.0000 chunk 58 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 53 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 47 optimal weight: 30.0000 chunk 59 optimal weight: 0.0870 chunk 106 optimal weight: 10.0000 overall best weight: 2.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 54 GLN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.106463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.085534 restraints weight = 31980.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.084694 restraints weight = 23930.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.086201 restraints weight = 18847.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.086337 restraints weight = 14469.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.086226 restraints weight = 13189.461| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8388 Z= 0.159 Angle : 0.497 6.109 11849 Z= 0.292 Chirality : 0.038 0.180 1516 Planarity : 0.003 0.034 1272 Dihedral : 15.963 163.497 2324 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.47 % Allowed : 24.38 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.63 (0.27), residues: 1008 helix: 1.95 (0.20), residues: 649 sheet: -1.49 (0.62), residues: 57 loop : -0.25 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 126 TYR 0.012 0.002 TYR C 111 PHE 0.016 0.002 PHE C 17 TRP 0.000 0.000 TRP D 522 HIS 0.006 0.001 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.16 ( 8388) covalent geometry : angle 0.49735 / 0.29 (11849) hydrogen bonds : bond 0.04434 / 3.05 ( 570) hydrogen bonds : angle 4.50966 / 3.42 ( 1576) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 716 LYS cc_start: 0.8495 (mttt) cc_final: 0.8046 (mttm) REVERT: D 108 MET cc_start: 0.8336 (mmm) cc_final: 0.7964 (mmm) REVERT: C 98 GLN cc_start: 0.8543 (tm-30) cc_final: 0.8318 (tm-30) REVERT: C 102 ASP cc_start: 0.7603 (p0) cc_final: 0.7289 (p0) REVERT: C 123 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7820 (mm) REVERT: C 126 ARG cc_start: 0.7723 (tmt170) cc_final: 0.6786 (tmm-80) outliers start: 8 outliers final: 5 residues processed: 99 average time/residue: 0.0765 time to fit residues: 10.5365 Evaluate side-chains 92 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 735 GLN Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 123 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 67 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 95 optimal weight: 20.0000 chunk 82 optimal weight: 0.7980 chunk 48 optimal weight: 30.0000 chunk 104 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.105566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.085263 restraints weight = 32425.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.085175 restraints weight = 23238.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.086522 restraints weight = 17793.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.086441 restraints weight = 15465.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.086362 restraints weight = 12965.666| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8388 Z= 0.171 Angle : 0.502 7.938 11849 Z= 0.290 Chirality : 0.038 0.215 1516 Planarity : 0.003 0.035 1272 Dihedral : 15.968 160.898 2324 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.86 % Allowed : 21.60 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.83 (0.27), residues: 1008 helix: 2.10 (0.21), residues: 651 sheet: -1.44 (0.60), residues: 60 loop : -0.13 (0.38), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 126 TYR 0.013 0.002 TYR C 96 PHE 0.016 0.002 PHE C 17 TRP 0.000 0.000 TRP D 522 HIS 0.003 0.001 HIS D 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 ( 8388) covalent geometry : angle 0.50202 / 0.29 (11849) hydrogen bonds : bond 0.04386 / 3.03 ( 570) hydrogen bonds : angle 4.29866 / 3.26 ( 1576) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 716 LYS cc_start: 0.8527 (mttt) cc_final: 0.8080 (mttm) REVERT: B 736 ARG cc_start: 0.8997 (tmm-80) cc_final: 0.8650 (tpt-90) REVERT: C 116 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7588 (mt-10) REVERT: C 123 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7838 (mm) REVERT: C 126 ARG cc_start: 0.7775 (tmt170) cc_final: 0.6850 (tmm-80) outliers start: 19 outliers final: 11 residues processed: 106 average time/residue: 0.0577 time to fit residues: 8.6444 Evaluate side-chains 100 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 735 GLN Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain C residue 12 MET Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 167 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 32 optimal weight: 6.9990 chunk 90 optimal weight: 40.0000 chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 93 optimal weight: 30.0000 chunk 11 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 89 optimal weight: 40.0000 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 132 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.105801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.082605 restraints weight = 32378.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.084387 restraints weight = 19652.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.085482 restraints weight = 14332.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.086112 restraints weight = 11834.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.086405 restraints weight = 10582.431| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8388 Z= 0.152 Angle : 0.499 8.340 11849 Z= 0.285 Chirality : 0.038 0.179 1516 Planarity : 0.003 0.036 1272 Dihedral : 16.048 161.785 2324 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.68 % Favored : 97.12 % Rotamer: Outliers : 3.70 % Allowed : 26.85 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1008 helix: 2.20 (0.21), residues: 646 sheet: -1.02 (0.60), residues: 55 loop : 0.03 (0.38), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 126 TYR 0.017 0.002 TYR C 96 PHE 0.017 0.002 PHE C 104 TRP 0.000 0.000 TRP D 522 HIS 0.002 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 8388) covalent geometry : angle 0.49895 / 0.28 (11849) hydrogen bonds : bond 0.04108 / 2.82 ( 570) hydrogen bonds : angle 4.17226 / 3.17 ( 1576) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: B 716 LYS cc_start: 0.8521 (mttt) cc_final: 0.8057 (mttm) REVERT: B 736 ARG cc_start: 0.8966 (tmm-80) cc_final: 0.8517 (tpt-90) REVERT: B 739 GLU cc_start: 0.8278 (pp20) cc_final: 0.7684 (pp20) REVERT: C 73 ASP cc_start: 0.8094 (p0) cc_final: 0.7708 (p0) REVERT: C 123 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7745 (mm) REVERT: C 126 ARG cc_start: 0.7651 (tmt170) cc_final: 0.6832 (tmm-80) outliers start: 12 outliers final: 8 residues processed: 104 average time/residue: 0.0642 time to fit residues: 9.5957 Evaluate side-chains 103 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain C residue 12 MET Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 123 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 69 optimal weight: 0.8980 chunk 81 optimal weight: 20.0000 chunk 44 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 79 optimal weight: 20.0000 chunk 63 optimal weight: 0.0170 chunk 40 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.104370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.083110 restraints weight = 30207.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.082675 restraints weight = 20306.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.083737 restraints weight = 15530.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.084078 restraints weight = 12438.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.084107 restraints weight = 11271.063| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 8388 Z= 0.107 Angle : 0.468 8.110 11849 Z= 0.266 Chirality : 0.037 0.179 1516 Planarity : 0.003 0.037 1272 Dihedral : 16.051 160.997 2324 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.18 % Favored : 97.62 % Rotamer: Outliers : 3.70 % Allowed : 27.16 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.23 (0.28), residues: 1008 helix: 2.32 (0.21), residues: 644 sheet: -0.91 (0.60), residues: 55 loop : 0.19 (0.38), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 47 TYR 0.018 0.002 TYR C 103 PHE 0.017 0.002 PHE C 104 TRP 0.000 0.000 TRP D 522 HIS 0.002 0.001 HIS D 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 ( 8388) covalent geometry : angle 0.46791 / 0.27 (11849) hydrogen bonds : bond 0.03726 / 2.54 ( 570) hydrogen bonds : angle 4.00434 / 3.04 ( 1576) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.209 Fit side-chains REVERT: B 716 LYS cc_start: 0.8529 (mttt) cc_final: 0.8075 (mttm) REVERT: B 736 ARG cc_start: 0.9099 (tmm-80) cc_final: 0.8720 (tpt-90) REVERT: B 739 GLU cc_start: 0.8273 (pp20) cc_final: 0.7645 (pp20) REVERT: C 63 GLN cc_start: 0.7737 (mt0) cc_final: 0.7467 (tt0) REVERT: C 73 ASP cc_start: 0.8176 (p0) cc_final: 0.7830 (p0) REVERT: C 116 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7629 (mm-30) REVERT: C 123 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7806 (mm) REVERT: C 126 ARG cc_start: 0.7544 (tmt170) cc_final: 0.6656 (tmm-80) outliers start: 12 outliers final: 8 residues processed: 112 average time/residue: 0.0682 time to fit residues: 10.4229 Evaluate side-chains 105 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain C residue 12 MET Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 123 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 13 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 chunk 88 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 132 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.101570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.079570 restraints weight = 30930.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.079263 restraints weight = 22383.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.080452 restraints weight = 16859.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.080669 restraints weight = 14123.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.080610 restraints weight = 12556.293| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8388 Z= 0.231 Angle : 0.567 8.181 11849 Z= 0.319 Chirality : 0.039 0.180 1516 Planarity : 0.004 0.046 1272 Dihedral : 16.075 161.912 2324 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.88 % Favored : 96.92 % Rotamer: Outliers : 4.32 % Allowed : 26.85 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.98 (0.27), residues: 1008 helix: 2.09 (0.21), residues: 645 sheet: -0.86 (0.61), residues: 55 loop : 0.15 (0.38), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 47 TYR 0.015 0.002 TYR C 64 PHE 0.020 0.003 PHE C 60 TRP 0.000 0.000 TRP D 522 HIS 0.004 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.23 ( 8388) covalent geometry : angle 0.56678 / 0.32 (11849) hydrogen bonds : bond 0.04745 / 3.29 ( 570) hydrogen bonds : angle 4.24168 / 3.22 ( 1576) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: B 716 LYS cc_start: 0.8513 (mttt) cc_final: 0.8008 (mttm) REVERT: B 736 ARG cc_start: 0.9117 (tmm-80) cc_final: 0.8783 (tpt-90) REVERT: B 739 GLU cc_start: 0.8281 (pp20) cc_final: 0.7676 (pp20) REVERT: C 63 GLN cc_start: 0.7835 (mt0) cc_final: 0.7597 (tt0) REVERT: C 73 ASP cc_start: 0.8223 (p0) cc_final: 0.7716 (p0) REVERT: C 123 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7838 (mm) REVERT: C 126 ARG cc_start: 0.7893 (tmt170) cc_final: 0.7124 (tmm-80) outliers start: 14 outliers final: 11 residues processed: 107 average time/residue: 0.0699 time to fit residues: 10.4181 Evaluate side-chains 101 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain C residue 12 MET Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 167 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 83 optimal weight: 20.0000 chunk 95 optimal weight: 0.9980 chunk 55 optimal weight: 30.0000 chunk 88 optimal weight: 8.9990 chunk 29 optimal weight: 20.0000 chunk 68 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 99 optimal weight: 0.0970 chunk 53 optimal weight: 20.0000 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.105673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.082497 restraints weight = 32081.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.084295 restraints weight = 19569.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.085449 restraints weight = 14333.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.086027 restraints weight = 11793.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.086471 restraints weight = 10577.736| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8388 Z= 0.123 Angle : 0.500 8.903 11849 Z= 0.282 Chirality : 0.037 0.176 1516 Planarity : 0.003 0.040 1272 Dihedral : 16.144 161.657 2324 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.38 % Favored : 97.42 % Rotamer: Outliers : 3.40 % Allowed : 27.78 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.25 (0.28), residues: 1008 helix: 2.29 (0.21), residues: 643 sheet: -0.87 (0.61), residues: 55 loop : 0.32 (0.38), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 47 TYR 0.018 0.002 TYR C 161 PHE 0.014 0.002 PHE D 17 TRP 0.000 0.000 TRP D 522 HIS 0.002 0.001 HIS D 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 8388) covalent geometry : angle 0.50042 / 0.28 (11849) hydrogen bonds : bond 0.03841 / 2.63 ( 570) hydrogen bonds : angle 4.04801 / 3.08 ( 1576) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.207 Fit side-chains REVERT: B 716 LYS cc_start: 0.8536 (mttt) cc_final: 0.8029 (mttm) REVERT: B 736 ARG cc_start: 0.9058 (tmm-80) cc_final: 0.8675 (tpt-90) REVERT: B 739 GLU cc_start: 0.8198 (pp20) cc_final: 0.7613 (pp20) REVERT: C 73 ASP cc_start: 0.8104 (p0) cc_final: 0.7751 (p0) REVERT: C 123 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7603 (mm) REVERT: C 126 ARG cc_start: 0.7755 (tmt170) cc_final: 0.6874 (tmm-80) outliers start: 11 outliers final: 9 residues processed: 103 average time/residue: 0.0696 time to fit residues: 9.9681 Evaluate side-chains 99 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain C residue 12 MET Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 123 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 50.0000 chunk 2 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 30.0000 chunk 65 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.101847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.080241 restraints weight = 30510.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.079783 restraints weight = 20803.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.081028 restraints weight = 15944.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.081141 restraints weight = 13196.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.081139 restraints weight = 11649.340| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8388 Z= 0.183 Angle : 0.533 7.499 11849 Z= 0.301 Chirality : 0.038 0.174 1516 Planarity : 0.004 0.039 1272 Dihedral : 16.134 161.738 2324 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.88 % Favored : 96.92 % Rotamer: Outliers : 3.40 % Allowed : 27.47 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.13 (0.27), residues: 1008 helix: 2.15 (0.21), residues: 649 sheet: -0.86 (0.62), residues: 55 loop : 0.34 (0.38), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 47 TYR 0.012 0.002 TYR C 64 PHE 0.016 0.002 PHE C 17 TRP 0.000 0.000 TRP D 522 HIS 0.003 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.18 ( 8388) covalent geometry : angle 0.53255 / 0.30 (11849) hydrogen bonds : bond 0.04303 / 2.95 ( 570) hydrogen bonds : angle 4.11646 / 3.13 ( 1576) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.253 Fit side-chains REVERT: B 716 LYS cc_start: 0.8518 (mttt) cc_final: 0.7962 (mttm) REVERT: B 736 ARG cc_start: 0.9136 (tmm-80) cc_final: 0.8904 (tpt-90) REVERT: D 108 MET cc_start: 0.8538 (tpp) cc_final: 0.8156 (mmm) REVERT: C 73 ASP cc_start: 0.8174 (p0) cc_final: 0.7689 (p0) REVERT: C 123 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7745 (mm) REVERT: C 126 ARG cc_start: 0.7930 (tmt170) cc_final: 0.7117 (tmm-80) outliers start: 11 outliers final: 10 residues processed: 99 average time/residue: 0.0624 time to fit residues: 8.6875 Evaluate side-chains 100 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain C residue 12 MET Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 167 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 68 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 91 optimal weight: 50.0000 chunk 43 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 73 optimal weight: 0.2980 chunk 56 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 32 optimal weight: 4.9990 chunk 55 optimal weight: 30.0000 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.105390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.082307 restraints weight = 32034.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.084096 restraints weight = 19348.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.085181 restraints weight = 14173.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.085893 restraints weight = 11731.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.086298 restraints weight = 10467.354| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8388 Z= 0.128 Angle : 0.517 8.931 11849 Z= 0.291 Chirality : 0.037 0.170 1516 Planarity : 0.004 0.063 1272 Dihedral : 16.165 161.813 2324 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.48 % Favored : 97.22 % Rotamer: Outliers : 3.70 % Allowed : 27.47 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.28 (0.27), residues: 1008 helix: 2.26 (0.21), residues: 653 sheet: -0.88 (0.63), residues: 55 loop : 0.40 (0.39), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 724 TYR 0.013 0.001 TYR C 161 PHE 0.013 0.002 PHE D 17 TRP 0.000 0.000 TRP D 522 HIS 0.003 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 8388) covalent geometry : angle 0.51734 / 0.29 (11849) hydrogen bonds : bond 0.03856 / 2.63 ( 570) hydrogen bonds : angle 4.01680 / 3.05 ( 1576) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.170 Fit side-chains REVERT: B 716 LYS cc_start: 0.8530 (mttt) cc_final: 0.7974 (mttm) REVERT: B 736 ARG cc_start: 0.9066 (tmm-80) cc_final: 0.8682 (tpt-90) REVERT: B 739 GLU cc_start: 0.8126 (pp20) cc_final: 0.7545 (pp20) REVERT: D 108 MET cc_start: 0.8504 (tpp) cc_final: 0.8163 (mmm) REVERT: C 73 ASP cc_start: 0.8147 (p0) cc_final: 0.7729 (p0) REVERT: C 123 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7618 (mm) REVERT: C 126 ARG cc_start: 0.7800 (tmt170) cc_final: 0.6950 (tmm-80) outliers start: 12 outliers final: 11 residues processed: 103 average time/residue: 0.0593 time to fit residues: 8.7944 Evaluate side-chains 104 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain C residue 12 MET Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 167 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.0050 chunk 39 optimal weight: 9.9990 chunk 63 optimal weight: 0.0980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 81 optimal weight: 20.0000 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.103958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.083172 restraints weight = 30320.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.083536 restraints weight = 18903.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.084303 restraints weight = 14336.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.084560 restraints weight = 12551.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.084498 restraints weight = 11169.554| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8388 Z= 0.105 Angle : 0.500 8.495 11849 Z= 0.281 Chirality : 0.036 0.153 1516 Planarity : 0.003 0.055 1272 Dihedral : 16.127 161.716 2324 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.08 % Favored : 97.62 % Rotamer: Outliers : 2.47 % Allowed : 28.40 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.42 (0.28), residues: 1008 helix: 2.32 (0.21), residues: 655 sheet: -0.69 (0.65), residues: 55 loop : 0.53 (0.39), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 724 TYR 0.017 0.001 TYR C 161 PHE 0.015 0.002 PHE C 42 TRP 0.000 0.000 TRP D 522 HIS 0.002 0.000 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.11 ( 8388) covalent geometry : angle 0.50001 / 0.28 (11849) hydrogen bonds : bond 0.03485 / 2.37 ( 570) hydrogen bonds : angle 3.84519 / 2.92 ( 1576) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1169.49 seconds wall clock time: 20 minutes 46.23 seconds (1246.23 seconds total)