Starting phenix.real_space_refine on Sun Jul 5 13:52:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7oi0_12916/07_2026/7oi0_12916.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oi0_12916/07_2026/7oi0_12916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7oi0_12916/07_2026/7oi0_12916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oi0_12916/07_2026/7oi0_12916.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7oi0_12916/07_2026/7oi0_12916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oi0_12916/07_2026/7oi0_12916.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7oi0_12916/07_2026/7oi0_12916.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7oi0_12916/07_2026/7oi0_12916.cif" } resolution = 2.76 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= 0.007 sd= 0.083 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 963 5.49 5 S 30 5.16 5 C 14335 2.51 5 N 5400 2.21 5 O 8527 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s 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: 29255 Number of models: 1 Model: "" Number of chains: 17 Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "F" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "K" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 702 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "L" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "O" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 716 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 407 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "T" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "A" Number of atoms: 20700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 963, 20700 Classifications: {'RNA': 963} Modifications used: {'rna2p_pur': 74, 'rna2p_pyr': 44, 'rna3p_pur': 487, 'rna3p_pyr': 358} Link IDs: {'rna2p': 118, 'rna3p': 844} Chain breaks: 2 Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "L" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "P" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "Q" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "A" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 337 Classifications: {'water': 337} Link IDs: {None: 336} Time building chain proxies: 6.03, per 1000 atoms: 0.21 Number of scatterers: 29255 At special positions: 0 Unit cell: (111.8, 155.66, 212.42, 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 30 16.00 P 963 15.00 O 8527 8.00 N 5400 7.00 C 14335 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: 2.58 Conformation dependent library (CDL) restraints added in 605.5 milliseconds 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1930 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 11 sheets defined 39.9% alpha, 15.9% beta 338 base pairs and 532 stacking pairs defined. Time for finding SS restraints: 4.79 Creating SS restraints... Processing helix chain 'D' and resid 6 through 14 removed outlier: 3.928A pdb=" N LEU D 10 " --> pdb=" O PRO D 6 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU D 14 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 65 Processing helix chain 'D' and resid 67 through 81 Processing helix chain 'D' and resid 84 through 95 Processing helix chain 'D' and resid 96 through 104 Processing helix chain 'D' and resid 109 through 119 Processing helix chain 'D' and resid 146 through 149 Processing helix chain 'D' and resid 151 through 160 removed outlier: 3.603A pdb=" N GLU D 159 " --> pdb=" O LYS D 155 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 160 " --> pdb=" O ALA D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 203 removed outlier: 4.030A pdb=" N ILE D 199 " --> pdb=" O ASN D 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 16 No H-bonds generated for 'chain 'F' and resid 14 through 16' Processing helix chain 'F' and resid 17 through 32 Processing helix chain 'F' and resid 50 through 54 removed outlier: 3.640A pdb=" N LYS F 53 " --> pdb=" O PRO F 50 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU F 54 " --> pdb=" O ILE F 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 50 through 54' Processing helix chain 'F' and resid 69 through 81 removed outlier: 4.153A pdb=" N GLU F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU F 74 " --> pdb=" O VAL F 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 19 removed outlier: 3.694A pdb=" N MET H 9 " --> pdb=" O PRO H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 42 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 111 through 119 Processing helix chain 'K' and resid 58 through 72 Processing helix chain 'K' and resid 91 through 101 Processing helix chain 'L' and resid 2 through 9 Processing helix chain 'O' and resid 3 through 14 Processing helix chain 'O' and resid 23 through 46 removed outlier: 4.111A pdb=" N ALA O 43 " --> pdb=" O GLN O 39 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N GLU O 44 " --> pdb=" O GLY O 40 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N HIS O 45 " --> pdb=" O HIS O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 73 removed outlier: 3.678A pdb=" N ARG O 53 " --> pdb=" O HIS O 49 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLY O 54 " --> pdb=" O HIS O 50 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU O 55 " --> pdb=" O SER O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 84 removed outlier: 5.012A pdb=" N GLU O 82 " --> pdb=" O THR O 78 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 63 removed outlier: 3.845A pdb=" N ILE P 57 " --> pdb=" O ASP P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 82 Processing helix chain 'R' and resid 25 through 32 removed outlier: 3.662A pdb=" N LYS R 29 " --> pdb=" O ALA R 26 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ASN R 30 " --> pdb=" O THR R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 64 Processing helix chain 'T' and resid 3 through 39 Processing helix chain 'T' and resid 42 through 63 Proline residue: T 55 - end of helix Processing helix chain 'T' and resid 67 through 86 Processing sheet with id=AA1, first strand: chain 'D' and resid 127 through 128 Processing sheet with id=AA2, first strand: chain 'F' and resid 2 through 3 Processing sheet with id=AA3, first strand: chain 'F' and resid 40 through 46 removed outlier: 3.736A pdb=" N GLU F 40 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU F 61 " --> pdb=" O GLU F 40 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG F 44 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ALA F 57 " --> pdb=" O ARG F 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 23 through 24 Processing sheet with id=AA5, first strand: chain 'H' and resid 50 through 51 Processing sheet with id=AA6, first strand: chain 'H' and resid 75 through 76 Processing sheet with id=AA7, first strand: chain 'H' and resid 75 through 76 removed outlier: 6.900A pdb=" N VAL H 102 " --> pdb=" O ILE H 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 40 through 45 removed outlier: 6.645A pdb=" N ILE K 33 " --> pdb=" O LEU K 41 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TRP K 43 " --> pdb=" O VAL K 31 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL K 31 " --> pdb=" O TRP K 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 28 through 31 removed outlier: 10.174A pdb=" N VAL L 92 " --> pdb=" O GLU L 61 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N THR L 63 " --> pdb=" O VAL L 92 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TYR L 94 " --> pdb=" O THR L 63 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'P' and resid 50 through 51 removed outlier: 4.865A pdb=" N VAL P 19 " --> pdb=" O VAL P 36 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N PHE P 38 " --> pdb=" O TYR P 17 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TYR P 17 " --> pdb=" O PHE P 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Q' and resid 7 through 16 removed outlier: 7.901A pdb=" N GLN Q 8 " --> pdb=" O GLU Q 25 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N GLU Q 25 " --> pdb=" O GLN Q 8 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL Q 21 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ASP Q 14 " --> pdb=" O SER Q 19 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N SER Q 19 " --> pdb=" O ASP Q 14 " (cutoff:3.500A) removed outlier: 15.667A pdb=" N LYS Q 70 " --> pdb=" O THR Q 40 " (cutoff:3.500A) removed outlier: 14.072A pdb=" N LYS Q 42 " --> pdb=" O LYS Q 70 " (cutoff:3.500A) removed outlier: 9.785A pdb=" N TRP Q 72 " --> pdb=" O LYS Q 42 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N HIS Q 44 " --> pdb=" O TRP Q 72 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU Q 74 " --> pdb=" O HIS Q 44 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N HIS Q 46 " --> pdb=" O LEU Q 74 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N ARG Q 76 " --> pdb=" O HIS Q 46 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N SER Q 71 " --> pdb=" O CYS Q 63 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLU Q 59 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL Q 77 " --> pdb=" O VAL Q 57 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL Q 57 " --> pdb=" O VAL Q 77 " (cutoff:3.500A) 363 hydrogen bonds defined for protein. 1023 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 840 hydrogen bonds 1286 hydrogen bond angles 0 basepair planarities 338 basepair parallelities 532 stacking parallelities Total time for adding SS restraints: 11.96 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2788 1.30 - 1.43: 14063 1.43 - 1.56: 12652 1.56 - 1.68: 1924 1.68 - 1.81: 51 Bond restraints: 31478 Sorted by residual: bond pdb=" CB VAL P 20 " pdb=" CG2 VAL P 20 " ideal model delta sigma weight residual 1.521 1.404 0.117 3.30e-02 9.18e+02 1.25e+01 bond pdb=" C5 G A 108 " pdb=" C6 G A 108 " ideal model delta sigma weight residual 1.419 1.350 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" N ILE T 66 " pdb=" CA ILE T 66 " ideal model delta sigma weight residual 1.456 1.491 -0.036 1.11e-02 8.12e+03 1.03e+01 bond pdb=" N9 A A 452 " pdb=" C4 A A 452 " ideal model delta sigma weight residual 1.374 1.310 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" CD2 HIS P 9 " pdb=" NE2 HIS P 9 " ideal model delta sigma weight residual 1.374 1.339 0.035 1.10e-02 8.26e+03 9.97e+00 ... (remaining 31473 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 45535 2.52 - 5.04: 1588 5.04 - 7.57: 149 7.57 - 10.09: 17 10.09 - 12.61: 7 Bond angle restraints: 47296 Sorted by residual: angle pdb=" C4' G A 416 " pdb=" C3' G A 416 " pdb=" O3' G A 416 " ideal model delta sigma weight residual 113.00 125.61 -12.61 1.50e+00 4.44e-01 7.07e+01 angle pdb=" O2' G A 416 " pdb=" C2' G A 416 " pdb=" C1' G A 416 " ideal model delta sigma weight residual 108.40 97.74 10.66 1.50e+00 4.44e-01 5.05e+01 angle pdb=" C4' A A 465 " pdb=" C3' A A 465 " pdb=" O3' A A 465 " ideal model delta sigma weight residual 113.00 123.41 -10.41 1.50e+00 4.44e-01 4.82e+01 angle pdb=" C4' A A 415 " pdb=" C3' A A 415 " pdb=" O3' A A 415 " ideal model delta sigma weight residual 113.00 121.46 -8.46 1.50e+00 4.44e-01 3.18e+01 angle pdb=" O4' A A 182 " pdb=" C1' A A 182 " pdb=" N9 A A 182 " ideal model delta sigma weight residual 108.20 116.16 -7.96 1.50e+00 4.44e-01 2.82e+01 ... (remaining 47291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 15843 35.35 - 70.70: 779 70.70 - 106.05: 69 106.05 - 141.39: 7 141.39 - 176.74: 11 Dihedral angle restraints: 16709 sinusoidal: 13723 harmonic: 2986 Sorted by residual: dihedral pdb=" O4' U A 610 " pdb=" C1' U A 610 " pdb=" N1 U A 610 " pdb=" C2 U A 610 " ideal model delta sinusoidal sigma weight residual -160.00 5.95 -165.95 1 1.50e+01 4.44e-03 8.41e+01 dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 50.60 149.40 1 1.50e+01 4.44e-03 7.94e+01 dihedral pdb=" O4' C A 754 " pdb=" C1' C A 754 " pdb=" N1 C A 754 " pdb=" C2 C A 754 " ideal model delta sinusoidal sigma weight residual 200.00 50.65 149.35 1 1.50e+01 4.44e-03 7.94e+01 ... (remaining 16706 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 5788 0.138 - 0.275: 254 0.275 - 0.413: 13 0.413 - 0.551: 0 0.551 - 0.689: 1 Chirality restraints: 6056 Sorted by residual: chirality pdb=" C3' A A 465 " pdb=" C4' A A 465 " pdb=" O3' A A 465 " pdb=" C2' A A 465 " both_signs ideal model delta sigma weight residual False -2.48 -1.79 -0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" CB VAL P 20 " pdb=" CA VAL P 20 " pdb=" CG1 VAL P 20 " pdb=" CG2 VAL P 20 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CB ILE L 66 " pdb=" CA ILE L 66 " pdb=" CG1 ILE L 66 " pdb=" CG2 ILE L 66 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.44e+00 ... (remaining 6053 not shown) Planarity restraints: 2401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A 335 " -0.069 2.00e-02 2.50e+03 3.65e-02 3.00e+01 pdb=" N1 C A 335 " 0.080 2.00e-02 2.50e+03 pdb=" C2 C A 335 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C A 335 " 0.008 2.00e-02 2.50e+03 pdb=" N3 C A 335 " -0.008 2.00e-02 2.50e+03 pdb=" C4 C A 335 " -0.005 2.00e-02 2.50e+03 pdb=" N4 C A 335 " -0.018 2.00e-02 2.50e+03 pdb=" C5 C A 335 " -0.006 2.00e-02 2.50e+03 pdb=" C6 C A 335 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 181 " -0.069 2.00e-02 2.50e+03 3.16e-02 2.75e+01 pdb=" N9 A A 181 " 0.072 2.00e-02 2.50e+03 pdb=" C8 A A 181 " 0.012 2.00e-02 2.50e+03 pdb=" N7 A A 181 " -0.013 2.00e-02 2.50e+03 pdb=" C5 A A 181 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A A 181 " -0.011 2.00e-02 2.50e+03 pdb=" N6 A A 181 " -0.009 2.00e-02 2.50e+03 pdb=" N1 A A 181 " -0.014 2.00e-02 2.50e+03 pdb=" C2 A A 181 " 0.009 2.00e-02 2.50e+03 pdb=" N3 A A 181 " 0.009 2.00e-02 2.50e+03 pdb=" C4 A A 181 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 438 " 0.064 2.00e-02 2.50e+03 3.21e-02 2.32e+01 pdb=" N1 U A 438 " -0.063 2.00e-02 2.50e+03 pdb=" C2 U A 438 " -0.014 2.00e-02 2.50e+03 pdb=" O2 U A 438 " -0.009 2.00e-02 2.50e+03 pdb=" N3 U A 438 " 0.015 2.00e-02 2.50e+03 pdb=" C4 U A 438 " 0.008 2.00e-02 2.50e+03 pdb=" O4 U A 438 " 0.014 2.00e-02 2.50e+03 pdb=" C5 U A 438 " 0.004 2.00e-02 2.50e+03 pdb=" C6 U A 438 " -0.020 2.00e-02 2.50e+03 ... (remaining 2398 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 729 2.56 - 3.15: 23322 3.15 - 3.73: 63512 3.73 - 4.32: 87681 4.32 - 4.90: 112427 Nonbonded interactions: 287671 Sorted by model distance: nonbonded pdb=" N2 G A 444 " pdb=" O2 C A 490 " model vdw 1.977 2.496 nonbonded pdb=" N2 G A 457 " pdb=" O2 C A 475 " model vdw 1.982 2.496 nonbonded pdb=" O6 G A 410 " pdb=" O2' U A 429 " model vdw 1.983 3.040 nonbonded pdb=" O2 C A 658 " pdb=" N2 G A 748 " model vdw 2.021 2.496 nonbonded pdb=" OD1 ASP D 98 " pdb=" N ASN D 99 " model vdw 2.025 3.120 ... (remaining 287666 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 7.460 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: 0.030 Extract box with map and model: 0.720 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 35.640 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:7.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 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 : 0.014 0.117 31478 Z= 0.729 Angle : 1.079 12.609 47296 Z= 0.566 Chirality : 0.063 0.689 6056 Planarity : 0.007 0.062 2401 Dihedral : 17.048 176.743 14779 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 23.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.23 % Favored : 89.77 % Rotamer: Outliers : 0.23 % Allowed : 0.23 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.24), residues: 1017 helix: -0.71 (0.26), residues: 379 sheet: -2.44 (0.38), residues: 147 loop : -2.14 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG P 14 TYR 0.027 0.003 TYR L 116 PHE 0.016 0.003 PHE P 39 TRP 0.016 0.002 TRP Q 72 HIS 0.013 0.002 HIS D 119 Details of bonding type rmsd/Z covalent geometry : bond 0.01402 / 0.73 (31478) covalent geometry : angle 1.07882 / 0.57 (47296) hydrogen bonds : bond 0.16612 / 10.88 ( 1201) hydrogen bonds : angle 5.63530 / 3.83 ( 2309) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 3 residues processed: 115 average time/residue: 0.7354 time to fit residues: 98.6029 Evaluate side-chains 105 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 102 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain O residue 67 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 30.0000 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 20.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 HIS ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 ASN L 4 ASN ** L 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 HIS ** O 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.157515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.131407 restraints weight = 50357.748| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 0.51 r_work: 0.3698 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31478 Z= 0.148 Angle : 0.643 9.893 47296 Z= 0.329 Chirality : 0.036 0.246 6056 Planarity : 0.005 0.052 2401 Dihedral : 16.165 177.464 12718 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.28 % Allowed : 10.84 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.25), residues: 1017 helix: 0.58 (0.26), residues: 385 sheet: -2.09 (0.38), residues: 159 loop : -1.90 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 76 TYR 0.014 0.002 TYR F 59 PHE 0.009 0.001 PHE D 106 TRP 0.006 0.001 TRP P 60 HIS 0.009 0.001 HIS O 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (31478) covalent geometry : angle 0.64299 / 0.33 (47296) hydrogen bonds : bond 0.09103 / 6.06 ( 1201) hydrogen bonds : angle 3.65363 / 2.48 ( 2309) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 9 MET cc_start: -0.2418 (pmt) cc_final: -0.2840 (pmm) outliers start: 11 outliers final: 2 residues processed: 124 average time/residue: 0.7325 time to fit residues: 105.8300 Evaluate side-chains 102 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 3 HIS Chi-restraints excluded: chain L residue 63 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 183 optimal weight: 30.0000 chunk 179 optimal weight: 50.0000 chunk 192 optimal weight: 60.0000 chunk 103 optimal weight: 3.9990 chunk 165 optimal weight: 20.0000 chunk 149 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 166 optimal weight: 20.0000 chunk 82 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 151 GLN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 HIS ** O 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 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 = 0.4353 r_free = 0.4353 target = 0.151680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.124330 restraints weight = 49505.369| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 1.04 r_work: 0.3576 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.075 31478 Z= 0.569 Angle : 0.907 11.960 47296 Z= 0.446 Chirality : 0.052 0.386 6056 Planarity : 0.007 0.075 2401 Dihedral : 16.551 179.359 12712 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 3.50 % Allowed : 13.52 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.25), residues: 1017 helix: 0.38 (0.25), residues: 386 sheet: -2.29 (0.39), residues: 160 loop : -1.86 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 116 TYR 0.025 0.003 TYR L 116 PHE 0.016 0.002 PHE D 106 TRP 0.014 0.002 TRP Q 72 HIS 0.018 0.002 HIS O 41 Details of bonding type rmsd/Z covalent geometry : bond 0.01114 / 0.57 (31478) covalent geometry : angle 0.90699 / 0.45 (47296) hydrogen bonds : bond 0.12071 / 8.15 ( 1201) hydrogen bonds : angle 3.78626 / 2.55 ( 2309) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 9 MET cc_start: -0.2182 (pmt) cc_final: -0.2713 (pmm) REVERT: H 79 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8167 (ptm-80) REVERT: L 107 LYS cc_start: 0.7338 (mppt) cc_final: 0.7106 (mppt) REVERT: Q 15 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7936 (mtmm) outliers start: 30 outliers final: 8 residues processed: 117 average time/residue: 0.7091 time to fit residues: 97.2288 Evaluate side-chains 103 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 3 HIS Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain Q residue 15 LYS Chi-restraints excluded: chain T residue 85 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 135 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 149 optimal weight: 0.5980 chunk 141 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 HIS ** L 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 HIS ** O 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 8 GLN ** 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 = 0.4389 r_free = 0.4389 target = 0.154346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.126801 restraints weight = 49522.470| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 0.74 r_work: 0.3621 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 31478 Z= 0.251 Angle : 0.657 12.339 47296 Z= 0.332 Chirality : 0.037 0.260 6056 Planarity : 0.005 0.049 2401 Dihedral : 16.004 179.314 12712 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.15 % Allowed : 15.62 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.26), residues: 1017 helix: 0.79 (0.26), residues: 386 sheet: -2.32 (0.40), residues: 153 loop : -1.74 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 116 TYR 0.015 0.002 TYR L 116 PHE 0.013 0.001 PHE P 32 TRP 0.008 0.001 TRP Q 72 HIS 0.010 0.001 HIS O 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.25 (31478) covalent geometry : angle 0.65705 / 0.33 (47296) hydrogen bonds : bond 0.09253 / 6.17 ( 1201) hydrogen bonds : angle 3.40937 / 2.29 ( 2309) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 9 residues processed: 122 average time/residue: 0.6316 time to fit residues: 90.2128 Evaluate side-chains 108 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain F residue 3 HIS Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain T residue 85 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 172 optimal weight: 10.0000 chunk 170 optimal weight: 50.0000 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 171 optimal weight: 30.0000 chunk 179 optimal weight: 50.0000 chunk 7 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 41 HIS ** Q 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 HIS T 12 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.154354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.128227 restraints weight = 49550.183| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 0.76 r_work: 0.3635 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 31478 Z= 0.256 Angle : 0.658 11.406 47296 Z= 0.332 Chirality : 0.037 0.259 6056 Planarity : 0.005 0.040 2401 Dihedral : 15.862 178.546 12712 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.03 % Allowed : 16.43 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.16 (0.26), residues: 1017 helix: 0.93 (0.26), residues: 388 sheet: -2.23 (0.39), residues: 153 loop : -1.70 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 116 TYR 0.014 0.002 TYR L 116 PHE 0.011 0.001 PHE P 32 TRP 0.008 0.001 TRP Q 72 HIS 0.016 0.002 HIS F 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.26 (31478) covalent geometry : angle 0.65787 / 0.33 (47296) hydrogen bonds : bond 0.09329 / 6.26 ( 1201) hydrogen bonds : angle 3.33210 / 2.24 ( 2309) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 9 MET cc_start: -0.2248 (pmt) cc_final: -0.2668 (pmm) outliers start: 26 outliers final: 12 residues processed: 119 average time/residue: 0.6953 time to fit residues: 96.8703 Evaluate side-chains 107 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain T residue 85 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 168 optimal weight: 50.0000 chunk 64 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 178 optimal weight: 50.0000 chunk 180 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 HIS ** L 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 HIS ** Q 8 GLN ** 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 = 0.4390 r_free = 0.4390 target = 0.154368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.127669 restraints weight = 49416.529| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 0.73 r_work: 0.3640 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 31478 Z= 0.254 Angle : 0.653 12.414 47296 Z= 0.329 Chirality : 0.037 0.257 6056 Planarity : 0.005 0.053 2401 Dihedral : 15.779 178.737 12712 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.26 % Allowed : 17.37 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.06 (0.26), residues: 1017 helix: 0.96 (0.26), residues: 389 sheet: -2.15 (0.41), residues: 149 loop : -1.63 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 116 TYR 0.017 0.002 TYR D 75 PHE 0.011 0.001 PHE P 32 TRP 0.008 0.001 TRP Q 72 HIS 0.005 0.001 HIS O 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.25 (31478) covalent geometry : angle 0.65313 / 0.33 (47296) hydrogen bonds : bond 0.09176 / 6.16 ( 1201) hydrogen bonds : angle 3.28119 / 2.20 ( 2309) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 67 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8576 (mp) REVERT: F 9 MET cc_start: -0.2330 (pmt) cc_final: -0.2808 (pmm) REVERT: H 79 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8187 (ptm-80) REVERT: L 85 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.7007 (ptt90) REVERT: P 5 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.7940 (ptp-170) outliers start: 28 outliers final: 16 residues processed: 116 average time/residue: 0.7177 time to fit residues: 97.4344 Evaluate side-chains 114 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain T residue 85 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 190 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 171 optimal weight: 30.0000 chunk 162 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 ASN ** L 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 8 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 = 0.4327 r_free = 0.4327 target = 0.150997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.124679 restraints weight = 48001.696| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 0.88 r_work: 0.3572 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 31478 Z= 0.347 Angle : 0.718 13.555 47296 Z= 0.359 Chirality : 0.041 0.267 6056 Planarity : 0.005 0.049 2401 Dihedral : 15.893 178.464 12712 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.73 % Allowed : 18.07 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.13 (0.26), residues: 1017 helix: 0.88 (0.26), residues: 389 sheet: -2.14 (0.39), residues: 151 loop : -1.66 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 116 TYR 0.018 0.002 TYR L 116 PHE 0.010 0.001 PHE P 32 TRP 0.011 0.001 TRP Q 72 HIS 0.006 0.001 HIS O 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00674 / 0.35 (31478) covalent geometry : angle 0.71827 / 0.36 (47296) hydrogen bonds : bond 0.09881 / 6.66 ( 1201) hydrogen bonds : angle 3.35788 / 2.25 ( 2309) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 67 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8601 (mp) REVERT: D 125 ASN cc_start: 0.8746 (m-40) cc_final: 0.8426 (m-40) REVERT: F 9 MET cc_start: -0.2028 (pmt) cc_final: -0.2589 (pmm) REVERT: H 79 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8241 (ptm-80) REVERT: L 85 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.6901 (ptt90) REVERT: P 5 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.7971 (ptp-170) outliers start: 32 outliers final: 18 residues processed: 118 average time/residue: 0.6381 time to fit residues: 88.4456 Evaluate side-chains 120 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain T residue 85 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 34 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 135 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 8 GLN ** 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 = 0.4347 r_free = 0.4347 target = 0.152211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.125730 restraints weight = 48138.043| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 0.65 r_work: 0.3601 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31478 Z= 0.219 Angle : 0.631 16.702 47296 Z= 0.319 Chirality : 0.036 0.254 6056 Planarity : 0.005 0.051 2401 Dihedral : 15.671 178.762 12712 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 3.03 % Allowed : 19.23 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.91 (0.26), residues: 1017 helix: 1.08 (0.26), residues: 389 sheet: -1.97 (0.42), residues: 146 loop : -1.58 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 116 TYR 0.022 0.002 TYR D 75 PHE 0.011 0.001 PHE P 32 TRP 0.007 0.001 TRP Q 72 HIS 0.006 0.001 HIS O 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.22 (31478) covalent geometry : angle 0.63101 / 0.32 (47296) hydrogen bonds : bond 0.08826 / 5.91 ( 1201) hydrogen bonds : angle 3.23602 / 2.17 ( 2309) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 67 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8536 (mp) REVERT: F 9 MET cc_start: -0.2034 (pmt) cc_final: -0.2592 (pmm) REVERT: H 79 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8153 (ptm-80) REVERT: L 61 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7087 (tm-30) REVERT: P 5 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.7830 (ptp-170) outliers start: 26 outliers final: 16 residues processed: 117 average time/residue: 0.6029 time to fit residues: 83.1609 Evaluate side-chains 114 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain T residue 85 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 chunk 75 optimal weight: 0.1980 chunk 188 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 95 optimal weight: 0.2980 chunk 167 optimal weight: 50.0000 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 71 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 = 0.4364 r_free = 0.4364 target = 0.153436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.127399 restraints weight = 48166.270| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 0.50 r_work: 0.3620 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 31478 Z= 0.134 Angle : 0.615 19.483 47296 Z= 0.310 Chirality : 0.034 0.356 6056 Planarity : 0.005 0.066 2401 Dihedral : 15.656 179.029 12712 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.68 % Allowed : 20.16 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.26), residues: 1017 helix: 1.25 (0.26), residues: 383 sheet: -2.02 (0.41), residues: 147 loop : -1.45 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 116 TYR 0.020 0.002 TYR F 25 PHE 0.012 0.001 PHE P 32 TRP 0.006 0.001 TRP Q 72 HIS 0.006 0.001 HIS O 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 (31478) covalent geometry : angle 0.61522 / 0.31 (47296) hydrogen bonds : bond 0.08625 / 5.77 ( 1201) hydrogen bonds : angle 3.22131 / 2.16 ( 2309) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 67 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8516 (mp) REVERT: F 9 MET cc_start: -0.2070 (pmt) cc_final: -0.2635 (pmm) REVERT: P 5 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.7825 (ptp-170) outliers start: 23 outliers final: 15 residues processed: 113 average time/residue: 0.6247 time to fit residues: 82.7736 Evaluate side-chains 112 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain T residue 85 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 155 optimal weight: 10.0000 chunk 195 optimal weight: 30.0000 chunk 19 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 HIS ** L 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 8 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 = 0.4353 r_free = 0.4353 target = 0.152800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.126579 restraints weight = 47786.078| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 0.55 r_work: 0.3617 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31478 Z= 0.200 Angle : 0.626 20.903 47296 Z= 0.315 Chirality : 0.035 0.250 6056 Planarity : 0.005 0.050 2401 Dihedral : 15.563 178.864 12712 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.56 % Allowed : 20.40 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.26), residues: 1017 helix: 1.23 (0.26), residues: 389 sheet: -1.92 (0.41), residues: 148 loop : -1.49 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 116 TYR 0.018 0.001 TYR D 75 PHE 0.011 0.001 PHE P 32 TRP 0.006 0.001 TRP Q 72 HIS 0.005 0.001 HIS O 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.20 (31478) covalent geometry : angle 0.62637 / 0.31 (47296) hydrogen bonds : bond 0.08694 / 5.83 ( 1201) hydrogen bonds : angle 3.20008 / 2.14 ( 2309) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 67 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8504 (mp) REVERT: F 9 MET cc_start: -0.1874 (pmt) cc_final: -0.2499 (pmm) REVERT: P 5 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.7808 (ptp-170) outliers start: 22 outliers final: 15 residues processed: 112 average time/residue: 0.6618 time to fit residues: 86.3038 Evaluate side-chains 112 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain T residue 85 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 111 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 97 optimal weight: 0.2980 chunk 56 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 35 optimal weight: 0.3980 chunk 7 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 71 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 = 0.4385 r_free = 0.4385 target = 0.154257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.128316 restraints weight = 48636.011| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 0.49 r_work: 0.3662 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31478 Z= 0.133 Angle : 0.601 20.152 47296 Z= 0.303 Chirality : 0.033 0.245 6056 Planarity : 0.005 0.058 2401 Dihedral : 15.530 179.042 12712 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.33 % Allowed : 20.86 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.60 (0.26), residues: 1017 helix: 1.37 (0.26), residues: 383 sheet: -1.82 (0.41), residues: 142 loop : -1.39 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 116 TYR 0.021 0.001 TYR F 25 PHE 0.010 0.001 PHE P 32 TRP 0.005 0.001 TRP Q 72 HIS 0.006 0.001 HIS F 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 (31478) covalent geometry : angle 0.60091 / 0.30 (47296) hydrogen bonds : bond 0.08425 / 5.63 ( 1201) hydrogen bonds : angle 3.18622 / 2.14 ( 2309) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8258.51 seconds wall clock time: 142 minutes 18.47 seconds (8538.47 seconds total)