Starting phenix.real_space_refine on Sun Jul 5 18:47:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8c98_16505/07_2026/8c98_16505.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c98_16505/07_2026/8c98_16505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c98_16505/07_2026/8c98_16505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c98_16505/07_2026/8c98_16505.map" model { file = "/net/cci-nas-00/data/ceres_data/8c98_16505/07_2026/8c98_16505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c98_16505/07_2026/8c98_16505.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8c98_16505/07_2026/8c98_16505.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8c98_16505/07_2026/8c98_16505.cif" } resolution = 3.66 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= 0.023 sd= 0.113 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 1017 5.49 5 S 20 5.16 5 C 15050 2.51 5 N 5646 2.21 5 O 8551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s 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: 30284 Number of models: 1 Model: "" Number of chains: 12 Chain: "2" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 286 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "E" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1454 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain breaks: 1 Chain: "J" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1055 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain breaks: 1 Chain: "L" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 671 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain breaks: 1 Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 734 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain breaks: 1 Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "A" Number of atoms: 21846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1018, 21846 Classifications: {'DNA': 1, 'RNA': 1017} Modifications used: {'rna2p_pur': 95, 'rna2p_pyr': 52, 'rna3p_pur': 499, 'rna3p_pyr': 371} Incomplete info: {'p_only': 1} Link IDs: {'rna2p': 147, 'rna3p': 870} Unresolved chain links: 2 Chain breaks: 6 Unresolved chain link angles: 11 Unresolved chain link dihedrals: 8 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {' G:plan': 1, ' G:plan2': 1} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 4.91, per 1000 atoms: 0.16 Number of scatterers: 30284 At special positions: 0 Unit cell: (131.25, 190, 167.5, 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 20 16.00 P 1017 15.00 O 8551 8.00 N 5646 7.00 C 15050 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: 1.97 Conformation dependent library (CDL) restraints added in 384.5 milliseconds 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2006 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 12 sheets defined 39.5% alpha, 13.6% beta 335 base pairs and 521 stacking pairs defined. Time for finding SS restraints: 4.64 Creating SS restraints... Processing helix chain '2' and resid 10 through 17 Processing helix chain '2' and resid 17 through 24 removed outlier: 3.894A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 24 through 38 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 39 Processing helix chain 'E' and resid 97 through 115 Processing helix chain 'E' and resid 130 through 141 Processing helix chain 'E' and resid 154 through 164 removed outlier: 4.359A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU E 164 " --> pdb=" O ALA E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 175 No H-bonds generated for 'chain 'E' and resid 173 through 175' Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 190 through 201 Processing helix chain 'J' and resid 25 through 37 Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 89 through 96 Processing helix chain 'J' and resid 97 through 108 removed outlier: 4.084A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 121 removed outlier: 3.655A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 136 removed outlier: 3.682A pdb=" N ALA J 134 " --> pdb=" O ASN J 131 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 136 removed outlier: 3.957A pdb=" N ALA L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 19 removed outlier: 3.916A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 29 removed outlier: 4.435A pdb=" N ARG Q 27 " --> pdb=" O TYR Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 70 removed outlier: 4.321A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN Q 70 " --> pdb=" O ALA Q 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 Processing helix chain 'Q' and resid 90 through 101 Processing helix chain 'Q' and resid 101 through 117 removed outlier: 4.000A pdb=" N PHE Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA Q 117 " --> pdb=" O LYS Q 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 23 removed outlier: 3.865A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 removed outlier: 3.860A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 62 removed outlier: 4.098A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 11 removed outlier: 3.840A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 removed outlier: 3.857A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 52 Processing helix chain 'Y' and resid 9 through 34 removed outlier: 3.809A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 56 removed outlier: 4.017A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 50 Processing sheet with id=AA1, first strand: chain 'E' and resid 118 through 121 removed outlier: 3.843A pdb=" N VAL E 121 " --> pdb=" O MET E 188 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL E 146 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ARG E 170 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE E 148 " --> pdb=" O ARG E 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 123 through 125 removed outlier: 6.306A pdb=" N ILE J 54 " --> pdb=" O LYS J 123 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N TYR J 125 " --> pdb=" O ILE J 54 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL J 56 " --> pdb=" O TYR J 125 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 23 through 24 removed outlier: 5.779A pdb=" N LYS J 23 " --> pdb=" O ALA J 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'J' and resid 73 through 74 Processing sheet with id=AA5, first strand: chain 'R' and resid 11 through 14 removed outlier: 6.870A pdb=" N GLN R 6 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL R 38 " --> pdb=" O GLN R 6 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 19 through 22 removed outlier: 7.023A pdb=" N PHE R 93 " --> pdb=" O HIS R 66 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N HIS R 66 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL R 64 " --> pdb=" O ASP R 95 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR R 99 " --> pdb=" O LYS R 60 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 72 through 75 Processing sheet with id=AA8, first strand: chain 'S' and resid 2 through 10 removed outlier: 5.611A pdb=" N SER S 101 " --> pdb=" O HIS S 9 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N HIS S 102 " --> pdb=" O VAL S 76 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL S 76 " --> pdb=" O HIS S 102 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR S 104 " --> pdb=" O ILE S 74 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE S 74 " --> pdb=" O THR S 104 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL S 106 " --> pdb=" O THR S 72 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'T' and resid 13 through 14 removed outlier: 4.033A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TRP T 80 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL T 62 " --> pdb=" O TRP T 80 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LYS T 82 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR T 60 " --> pdb=" O LYS T 82 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TYR T 84 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL T 58 " --> pdb=" O TYR T 84 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR T 86 " --> pdb=" O GLU T 56 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'U' and resid 64 through 65 removed outlier: 6.676A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'U' and resid 82 through 86 Processing sheet with id=AB3, first strand: chain 'Z' and resid 34 through 38 340 hydrogen bonds defined for protein. 981 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 853 hydrogen bonds 1378 hydrogen bond angles 0 basepair planarities 335 basepair parallelities 521 stacking parallelities Total time for adding SS restraints: 9.72 Time building geometry restraints manager: 2.75 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: 4501 1.33 - 1.45: 13501 1.45 - 1.57: 12918 1.57 - 1.69: 2027 1.69 - 1.81: 40 Bond restraints: 32987 Sorted by residual: bond pdb=" C1' U A 546 " pdb=" N1 U A 546 " ideal model delta sigma weight residual 1.480 1.573 -0.093 1.50e-02 4.44e+03 3.88e+01 bond pdb=" C1' U A 827 " pdb=" N1 U A 827 " ideal model delta sigma weight residual 1.480 1.573 -0.093 1.50e-02 4.44e+03 3.84e+01 bond pdb=" N MET Y 1 " pdb=" CA MET Y 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N MET J 1 " pdb=" CA MET J 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" N MET T 1 " pdb=" CA MET T 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 ... (remaining 32982 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 48869 1.22 - 2.43: 589 2.43 - 3.65: 84 3.65 - 4.87: 14 4.87 - 6.08: 2 Bond angle restraints: 49558 Sorted by residual: angle pdb=" N ALA S 64 " pdb=" CA ALA S 64 " pdb=" C ALA S 64 " ideal model delta sigma weight residual 107.73 112.44 -4.71 1.34e+00 5.57e-01 1.24e+01 angle pdb=" C4' U A1019 " pdb=" C3' U A1019 " pdb=" O3' U A1019 " ideal model delta sigma weight residual 109.40 113.45 -4.05 1.50e+00 4.44e-01 7.29e+00 angle pdb=" C3' U A1019 " pdb=" O3' U A1019 " pdb=" P A A1020 " ideal model delta sigma weight residual 120.20 123.94 -3.74 1.50e+00 4.44e-01 6.23e+00 angle pdb=" C4' A A 404 " pdb=" C3' A A 404 " pdb=" O3' A A 404 " ideal model delta sigma weight residual 109.40 112.81 -3.41 1.50e+00 4.44e-01 5.17e+00 angle pdb=" N LYS E 6 " pdb=" CA LYS E 6 " pdb=" CB LYS E 6 " ideal model delta sigma weight residual 113.65 110.36 3.29 1.47e+00 4.63e-01 5.00e+00 ... (remaining 49553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 16958 35.81 - 71.61: 461 71.61 - 107.42: 54 107.42 - 143.23: 7 143.23 - 179.04: 3 Dihedral angle restraints: 17483 sinusoidal: 14394 harmonic: 3089 Sorted by residual: dihedral pdb=" O4' C A 323 " pdb=" C1' C A 323 " pdb=" N1 C A 323 " pdb=" C2 C A 323 " ideal model delta sinusoidal sigma weight residual -128.00 29.07 -157.07 1 1.70e+01 3.46e-03 6.38e+01 dihedral pdb=" O4' U A1313 " pdb=" C1' U A1313 " pdb=" N1 U A1313 " pdb=" C2 U A1313 " ideal model delta sinusoidal sigma weight residual 200.00 98.74 101.26 1 1.50e+01 4.44e-03 5.10e+01 dihedral pdb=" C4' U A 276 " pdb=" C3' U A 276 " pdb=" O3' U A 276 " pdb=" P G A 277 " ideal model delta sinusoidal sigma weight residual 220.00 40.96 179.04 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 17480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 5571 0.036 - 0.072: 663 0.072 - 0.108: 125 0.108 - 0.143: 47 0.143 - 0.179: 2 Chirality restraints: 6408 Sorted by residual: chirality pdb=" C3' U A1019 " pdb=" C4' U A1019 " pdb=" O3' U A1019 " pdb=" C2' U A1019 " both_signs ideal model delta sigma weight residual False -2.74 -2.57 -0.18 2.00e-01 2.50e+01 8.03e-01 chirality pdb=" C1' U A 827 " pdb=" O4' U A 827 " pdb=" C2' U A 827 " pdb=" N1 U A 827 " both_signs ideal model delta sigma weight residual False 2.47 2.62 -0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" CA ILE S 103 " pdb=" N ILE S 103 " pdb=" C ILE S 103 " pdb=" CB ILE S 103 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 6405 not shown) Planarity restraints: 2468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 259 " 0.009 2.00e-02 2.50e+03 1.47e-02 6.47e+00 pdb=" N9 G A 259 " -0.002 2.00e-02 2.50e+03 pdb=" C8 G A 259 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G A 259 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G A 259 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G A 259 " -0.011 2.00e-02 2.50e+03 pdb=" O6 G A 259 " 0.013 2.00e-02 2.50e+03 pdb=" N1 G A 259 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G A 259 " -0.039 2.00e-02 2.50e+03 pdb=" N2 G A 259 " 0.025 2.00e-02 2.50e+03 pdb=" N3 G A 259 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G A 259 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 269 " -0.014 2.00e-02 2.50e+03 1.51e-02 5.13e+00 pdb=" N1 C A 269 " 0.017 2.00e-02 2.50e+03 pdb=" C2 C A 269 " 0.033 2.00e-02 2.50e+03 pdb=" O2 C A 269 " -0.019 2.00e-02 2.50e+03 pdb=" N3 C A 269 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C A 269 " 0.002 2.00e-02 2.50e+03 pdb=" N4 C A 269 " -0.006 2.00e-02 2.50e+03 pdb=" C5 C A 269 " -0.007 2.00e-02 2.50e+03 pdb=" C6 C A 269 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 239 " -0.009 2.00e-02 2.50e+03 1.44e-02 4.69e+00 pdb=" N1 C A 239 " 0.007 2.00e-02 2.50e+03 pdb=" C2 C A 239 " 0.035 2.00e-02 2.50e+03 pdb=" O2 C A 239 " -0.019 2.00e-02 2.50e+03 pdb=" N3 C A 239 " -0.004 2.00e-02 2.50e+03 pdb=" C4 C A 239 " 0.007 2.00e-02 2.50e+03 pdb=" N4 C A 239 " -0.009 2.00e-02 2.50e+03 pdb=" C5 C A 239 " -0.005 2.00e-02 2.50e+03 pdb=" C6 C A 239 " -0.002 2.00e-02 2.50e+03 ... (remaining 2465 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 241 2.52 - 3.11: 21985 3.11 - 3.71: 57922 3.71 - 4.30: 79359 4.30 - 4.90: 110115 Nonbonded interactions: 269622 Sorted by model distance: nonbonded pdb=" O2' A A 126 " pdb=" O4' A A 127 " model vdw 1.923 3.040 nonbonded pdb=" OD2 ASP Q 48 " pdb=" O2' U A 534 " model vdw 1.941 3.040 nonbonded pdb=" OP2 G A 117 " pdb=" O2' A A 119 " model vdw 1.983 3.040 nonbonded pdb=" O2' A A1383 " pdb=" O4' A A1384 " model vdw 1.996 3.040 nonbonded pdb=" O2' A A 299 " pdb=" O4' A A 300 " model vdw 2.004 3.040 ... (remaining 269617 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 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: 0.410 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 30.200 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.060 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:2.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.093 32987 Z= 0.096 Angle : 0.375 6.083 49558 Z= 0.199 Chirality : 0.027 0.179 6408 Planarity : 0.002 0.021 2468 Dihedral : 13.480 179.037 15477 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.28), residues: 1050 helix: 2.69 (0.27), residues: 369 sheet: 0.18 (0.43), residues: 155 loop : -0.16 (0.29), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 27 TYR 0.006 0.001 TYR T 84 PHE 0.005 0.001 PHE S 75 TRP 0.002 0.000 TRP R 92 HIS 0.005 0.001 HIS Y 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00170 / 0.10 (32987) covalent geometry : angle 0.37513 / 0.20 (49558) hydrogen bonds : bond 0.09130 / 6.38 ( 1193) hydrogen bonds : angle 4.23535 / 3.02 ( 2359) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 95 LEU cc_start: 0.4567 (pt) cc_final: 0.3917 (tt) REVERT: T 1 MET cc_start: 0.4070 (pmm) cc_final: 0.3846 (pmm) REVERT: Y 1 MET cc_start: 0.6249 (tpp) cc_final: 0.5874 (tpp) REVERT: Z 36 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6380 (mm-30) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1852 time to fit residues: 20.3445 Evaluate side-chains 41 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 50.0000 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 20.0000 overall best weight: 6.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 47 HIS Q 71 ASN R 6 GLN R 18 GLN S 61 ASN Y 41 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.050916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.036705 restraints weight = 288697.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.037358 restraints weight = 126615.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.037685 restraints weight = 87996.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.037950 restraints weight = 76445.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.038035 restraints weight = 70885.302| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 32987 Z= 0.277 Angle : 0.660 10.851 49558 Z= 0.329 Chirality : 0.035 0.208 6408 Planarity : 0.005 0.038 2468 Dihedral : 14.392 177.005 13361 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.68 % Allowed : 6.02 % Favored : 93.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.26), residues: 1050 helix: 1.25 (0.26), residues: 374 sheet: 0.17 (0.45), residues: 139 loop : -0.75 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 90 TYR 0.015 0.002 TYR J 53 PHE 0.022 0.002 PHE 2 18 TRP 0.005 0.001 TRP Q 60 HIS 0.007 0.002 HIS Z 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.28 (32987) covalent geometry : angle 0.66005 / 0.33 (49558) hydrogen bonds : bond 0.08007 / 5.43 ( 1193) hydrogen bonds : angle 3.78387 / 2.70 ( 2359) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.528 Fit side-chains REVERT: L 95 LEU cc_start: 0.4577 (pt) cc_final: 0.4241 (tt) REVERT: R 37 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7121 (tp30) REVERT: R 53 PHE cc_start: 0.7772 (m-10) cc_final: 0.7558 (m-80) REVERT: S 1 MET cc_start: 0.6526 (ttt) cc_final: 0.6246 (ttt) REVERT: T 1 MET cc_start: 0.3936 (pmm) cc_final: 0.3730 (pmm) outliers start: 6 outliers final: 4 residues processed: 53 average time/residue: 0.1595 time to fit residues: 14.9452 Evaluate side-chains 46 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain Z residue 4 ILE Chi-restraints excluded: chain Z residue 34 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... T 48 GLN ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN ** U 53 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 = 0.3654 r_free = 0.3654 target = 0.050484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.036562 restraints weight = 290307.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.037018 restraints weight = 132008.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.037404 restraints weight = 89353.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.037599 restraints weight = 75484.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.037683 restraints weight = 70252.274| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 32987 Z= 0.264 Angle : 0.592 9.890 49558 Z= 0.300 Chirality : 0.033 0.241 6408 Planarity : 0.004 0.033 2468 Dihedral : 14.453 169.175 13361 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.93 % Allowed : 8.41 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.25), residues: 1050 helix: 0.84 (0.26), residues: 381 sheet: 0.01 (0.43), residues: 145 loop : -0.97 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Y 52 TYR 0.010 0.002 TYR J 44 PHE 0.020 0.002 PHE 2 18 TRP 0.006 0.001 TRP J 15 HIS 0.009 0.001 HIS Z 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.26 (32987) covalent geometry : angle 0.59171 / 0.30 (49558) hydrogen bonds : bond 0.06664 / 4.54 ( 1193) hydrogen bonds : angle 3.67243 / 2.62 ( 2359) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.558 Fit side-chains REVERT: L 95 LEU cc_start: 0.4535 (pt) cc_final: 0.4097 (tt) REVERT: R 31 GLU cc_start: 0.8674 (pt0) cc_final: 0.8193 (pt0) REVERT: Z 36 GLU cc_start: 0.6738 (pp20) cc_final: 0.6405 (pp20) outliers start: 17 outliers final: 11 residues processed: 59 average time/residue: 0.1424 time to fit residues: 15.2725 Evaluate side-chains 51 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 16 HIS Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain Z residue 4 ILE Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 51 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 15 optimal weight: 7.9990 chunk 142 optimal weight: 40.0000 chunk 60 optimal weight: 9.9990 chunk 122 optimal weight: 20.0000 chunk 27 optimal weight: 0.2980 chunk 180 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 overall best weight: 7.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 7 HIS T 59 ASN ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 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 = 0.3636 r_free = 0.3636 target = 0.050170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.035933 restraints weight = 289826.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.036588 restraints weight = 129396.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.037020 restraints weight = 89780.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.037173 restraints weight = 76181.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.037333 restraints weight = 71696.995| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 32987 Z= 0.296 Angle : 0.645 11.190 49558 Z= 0.326 Chirality : 0.035 0.272 6408 Planarity : 0.005 0.034 2468 Dihedral : 14.921 176.333 13361 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 2.61 % Allowed : 10.80 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.25), residues: 1050 helix: 0.72 (0.26), residues: 373 sheet: -0.05 (0.42), residues: 150 loop : -1.20 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 2 12 TYR 0.011 0.002 TYR J 44 PHE 0.022 0.002 PHE 2 18 TRP 0.003 0.001 TRP Q 60 HIS 0.006 0.002 HIS Y 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.30 (32987) covalent geometry : angle 0.64476 / 0.33 (49558) hydrogen bonds : bond 0.07460 / 5.09 ( 1193) hydrogen bonds : angle 3.73241 / 2.65 ( 2359) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 43 time to evaluate : 0.579 Fit side-chains REVERT: L 95 LEU cc_start: 0.4664 (pt) cc_final: 0.4266 (tt) REVERT: R 34 GLU cc_start: 0.8157 (mp0) cc_final: 0.7718 (mp0) REVERT: Z 36 GLU cc_start: 0.6572 (pp20) cc_final: 0.6221 (pp20) outliers start: 23 outliers final: 18 residues processed: 63 average time/residue: 0.1395 time to fit residues: 15.9561 Evaluate side-chains 58 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 40 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain Z residue 4 ILE Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 56 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 49 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 194 optimal weight: 10.0000 chunk 8 optimal weight: 0.3980 chunk 83 optimal weight: 4.9990 chunk 199 optimal weight: 40.0000 chunk 85 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 53 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.050726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.037408 restraints weight = 289159.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.038216 restraints weight = 134567.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.037968 restraints weight = 93791.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.037958 restraints weight = 83023.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.038030 restraints weight = 82372.757| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 32987 Z= 0.126 Angle : 0.493 9.799 49558 Z= 0.255 Chirality : 0.030 0.253 6408 Planarity : 0.003 0.032 2468 Dihedral : 14.496 168.232 13361 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.70 % Allowed : 13.07 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.25), residues: 1050 helix: 1.14 (0.26), residues: 373 sheet: -0.16 (0.40), residues: 158 loop : -1.00 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 110 TYR 0.008 0.001 TYR E 101 PHE 0.008 0.001 PHE E 23 TRP 0.003 0.001 TRP J 15 HIS 0.003 0.001 HIS R 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.13 (32987) covalent geometry : angle 0.49276 / 0.26 (49558) hydrogen bonds : bond 0.05218 / 3.51 ( 1193) hydrogen bonds : angle 3.42306 / 2.47 ( 2359) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.474 Fit side-chains REVERT: L 95 LEU cc_start: 0.3769 (pt) cc_final: 0.3210 (tt) REVERT: Z 36 GLU cc_start: 0.6700 (pp20) cc_final: 0.6341 (pp20) outliers start: 15 outliers final: 10 residues processed: 56 average time/residue: 0.1579 time to fit residues: 15.5011 Evaluate side-chains 49 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 16 HIS Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 56 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 110 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 197 optimal weight: 30.0000 chunk 139 optimal weight: 40.0000 chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 70 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 = 0.3643 r_free = 0.3643 target = 0.050325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.036462 restraints weight = 288905.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.036910 restraints weight = 129873.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.037294 restraints weight = 88444.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.037459 restraints weight = 74988.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.037562 restraints weight = 70386.546| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 32987 Z= 0.239 Angle : 0.572 9.440 49558 Z= 0.291 Chirality : 0.033 0.255 6408 Planarity : 0.004 0.033 2468 Dihedral : 14.699 175.047 13361 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 2.73 % Allowed : 13.52 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.25), residues: 1050 helix: 0.88 (0.26), residues: 379 sheet: -0.27 (0.39), residues: 158 loop : -1.16 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 52 TYR 0.008 0.002 TYR J 44 PHE 0.018 0.002 PHE 2 18 TRP 0.003 0.001 TRP Q 60 HIS 0.004 0.001 HIS S 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.24 (32987) covalent geometry : angle 0.57152 / 0.29 (49558) hydrogen bonds : bond 0.06566 / 4.48 ( 1193) hydrogen bonds : angle 3.54317 / 2.52 ( 2359) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 44 time to evaluate : 0.603 Fit side-chains REVERT: L 95 LEU cc_start: 0.4089 (pt) cc_final: 0.3599 (tt) REVERT: R 37 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7547 (mm-30) REVERT: Z 36 GLU cc_start: 0.6604 (pp20) cc_final: 0.6060 (pp20) outliers start: 24 outliers final: 18 residues processed: 65 average time/residue: 0.1439 time to fit residues: 17.1123 Evaluate side-chains 59 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 16 HIS Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 56 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 176 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 117 optimal weight: 40.0000 chunk 183 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 175 optimal weight: 30.0000 chunk 64 optimal weight: 6.9990 chunk 33 optimal weight: 30.0000 overall best weight: 8.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 58 ASN J 128 ASN ** T 70 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 = 0.3630 r_free = 0.3630 target = 0.050025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.035842 restraints weight = 290388.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.036522 restraints weight = 127709.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.036958 restraints weight = 87828.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.037116 restraints weight = 74478.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.037255 restraints weight = 69974.683| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 32987 Z= 0.345 Angle : 0.666 15.852 49558 Z= 0.332 Chirality : 0.036 0.263 6408 Planarity : 0.005 0.039 2468 Dihedral : 14.813 175.274 13361 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 3.07 % Allowed : 14.89 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.25), residues: 1050 helix: 0.61 (0.26), residues: 385 sheet: -0.26 (0.40), residues: 152 loop : -1.41 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Y 52 TYR 0.013 0.002 TYR J 44 PHE 0.022 0.002 PHE 2 18 TRP 0.005 0.001 TRP Q 60 HIS 0.007 0.002 HIS Y 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00676 / 0.35 (32987) covalent geometry : angle 0.66621 / 0.33 (49558) hydrogen bonds : bond 0.07464 / 5.10 ( 1193) hydrogen bonds : angle 3.67249 / 2.61 ( 2359) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 41 time to evaluate : 0.659 Fit side-chains REVERT: L 95 LEU cc_start: 0.4195 (pt) cc_final: 0.3751 (tt) REVERT: T 1 MET cc_start: 0.4148 (pmm) cc_final: 0.3818 (pmm) REVERT: Z 36 GLU cc_start: 0.7240 (pp20) cc_final: 0.6901 (pp20) outliers start: 27 outliers final: 23 residues processed: 65 average time/residue: 0.1609 time to fit residues: 19.2036 Evaluate side-chains 63 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 40 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 16 HIS Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain Z residue 4 ILE Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 53 MET Chi-restraints excluded: chain Z residue 56 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 84 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 175 optimal weight: 30.0000 chunk 155 optimal weight: 10.0000 chunk 203 optimal weight: 40.0000 chunk 28 optimal weight: 0.0270 chunk 128 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 overall best weight: 6.2048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 70 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 = 0.3639 r_free = 0.3639 target = 0.050147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.036349 restraints weight = 291129.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.036767 restraints weight = 131054.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.037152 restraints weight = 89734.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.037342 restraints weight = 75289.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.037402 restraints weight = 70334.339| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 32987 Z= 0.247 Angle : 0.581 9.433 49558 Z= 0.297 Chirality : 0.033 0.287 6408 Planarity : 0.004 0.034 2468 Dihedral : 14.846 173.022 13361 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 2.73 % Allowed : 16.25 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.25), residues: 1050 helix: 0.66 (0.26), residues: 384 sheet: -0.27 (0.39), residues: 150 loop : -1.38 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Q 52 TYR 0.009 0.002 TYR J 44 PHE 0.016 0.002 PHE 2 18 TRP 0.004 0.001 TRP Q 60 HIS 0.004 0.001 HIS Y 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.25 (32987) covalent geometry : angle 0.58140 / 0.30 (49558) hydrogen bonds : bond 0.06343 / 4.32 ( 1193) hydrogen bonds : angle 3.58383 / 2.56 ( 2359) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 44 time to evaluate : 0.641 Fit side-chains REVERT: J 92 MET cc_start: 0.7168 (ttp) cc_final: 0.6697 (tpt) REVERT: L 95 LEU cc_start: 0.4117 (pt) cc_final: 0.3796 (tt) REVERT: Z 36 GLU cc_start: 0.6509 (pp20) cc_final: 0.6263 (pp20) outliers start: 24 outliers final: 21 residues processed: 65 average time/residue: 0.1682 time to fit residues: 19.4640 Evaluate side-chains 63 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 42 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 16 HIS Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 53 MET Chi-restraints excluded: chain Z residue 56 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 26 optimal weight: 6.9990 chunk 179 optimal weight: 20.0000 chunk 197 optimal weight: 30.0000 chunk 20 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 chunk 100 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 191 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 188 optimal weight: 30.0000 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 70 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 = 0.3639 r_free = 0.3639 target = 0.050160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.036374 restraints weight = 290903.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.036820 restraints weight = 131578.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.037217 restraints weight = 88969.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.037383 restraints weight = 75200.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.037500 restraints weight = 70407.266| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 32987 Z= 0.227 Angle : 0.573 9.369 49558 Z= 0.293 Chirality : 0.033 0.277 6408 Planarity : 0.004 0.034 2468 Dihedral : 14.874 174.309 13361 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.95 % Allowed : 16.70 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.25), residues: 1050 helix: 0.85 (0.26), residues: 377 sheet: -0.30 (0.39), residues: 150 loop : -1.34 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 69 TYR 0.008 0.002 TYR J 44 PHE 0.016 0.002 PHE 2 18 TRP 0.003 0.001 TRP J 15 HIS 0.004 0.001 HIS Y 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.23 (32987) covalent geometry : angle 0.57303 / 0.29 (49558) hydrogen bonds : bond 0.06455 / 4.39 ( 1193) hydrogen bonds : angle 3.58181 / 2.56 ( 2359) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 43 time to evaluate : 0.536 Fit side-chains REVERT: J 92 MET cc_start: 0.7042 (ttp) cc_final: 0.6538 (tpt) REVERT: L 95 LEU cc_start: 0.4256 (pt) cc_final: 0.3918 (tt) REVERT: U 67 SER cc_start: 0.8653 (OUTLIER) cc_final: 0.8450 (t) REVERT: Z 36 GLU cc_start: 0.6844 (pp20) cc_final: 0.6533 (pp20) outliers start: 26 outliers final: 20 residues processed: 67 average time/residue: 0.1604 time to fit residues: 19.7827 Evaluate side-chains 64 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 43 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 16 HIS Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 53 MET Chi-restraints excluded: chain Z residue 56 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 187 optimal weight: 10.0000 chunk 19 optimal weight: 0.0370 chunk 61 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 overall best weight: 5.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 70 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 = 0.3642 r_free = 0.3642 target = 0.050241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.036457 restraints weight = 289442.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.036885 restraints weight = 131286.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.037268 restraints weight = 88879.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.037437 restraints weight = 75273.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.037554 restraints weight = 70376.467| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 32987 Z= 0.213 Angle : 0.561 9.324 49558 Z= 0.286 Chirality : 0.032 0.276 6408 Planarity : 0.004 0.034 2468 Dihedral : 14.835 172.805 13361 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 2.50 % Allowed : 16.93 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.25), residues: 1050 helix: 0.76 (0.26), residues: 385 sheet: -0.24 (0.39), residues: 149 loop : -1.36 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 21 TYR 0.007 0.001 TYR S 38 PHE 0.014 0.002 PHE 2 18 TRP 0.003 0.001 TRP Q 60 HIS 0.004 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.21 (32987) covalent geometry : angle 0.56132 / 0.29 (49558) hydrogen bonds : bond 0.06094 / 4.15 ( 1193) hydrogen bonds : angle 3.54264 / 2.54 ( 2359) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 43 time to evaluate : 0.615 Fit side-chains REVERT: J 92 MET cc_start: 0.7074 (ttp) cc_final: 0.6528 (tpt) REVERT: L 95 LEU cc_start: 0.4059 (pt) cc_final: 0.3735 (tt) REVERT: T 1 MET cc_start: 0.3164 (pmm) cc_final: 0.2811 (pmm) REVERT: U 67 SER cc_start: 0.8650 (OUTLIER) cc_final: 0.8447 (t) REVERT: Z 36 GLU cc_start: 0.6831 (pp20) cc_final: 0.6548 (pp20) outliers start: 22 outliers final: 21 residues processed: 63 average time/residue: 0.1671 time to fit residues: 19.0764 Evaluate side-chains 63 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 41 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 16 HIS Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 53 MET Chi-restraints excluded: chain Z residue 56 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 72 optimal weight: 7.9990 chunk 178 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 174 optimal weight: 40.0000 chunk 200 optimal weight: 50.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 70 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 = 0.3621 r_free = 0.3621 target = 0.049882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.035721 restraints weight = 290803.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.036358 restraints weight = 129784.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.036761 restraints weight = 89925.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.036928 restraints weight = 76807.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.037045 restraints weight = 71895.727| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 32987 Z= 0.319 Angle : 0.655 9.192 49558 Z= 0.328 Chirality : 0.035 0.284 6408 Planarity : 0.005 0.040 2468 Dihedral : 14.991 174.991 13361 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 2.61 % Allowed : 17.27 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.24), residues: 1050 helix: 0.60 (0.26), residues: 381 sheet: -0.41 (0.40), residues: 149 loop : -1.57 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Y 52 TYR 0.014 0.002 TYR J 44 PHE 0.023 0.002 PHE 2 18 TRP 0.004 0.001 TRP Q 60 HIS 0.006 0.002 HIS E 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.32 (32987) covalent geometry : angle 0.65540 / 0.33 (49558) hydrogen bonds : bond 0.07450 / 5.09 ( 1193) hydrogen bonds : angle 3.67723 / 2.62 ( 2359) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5056.97 seconds wall clock time: 88 minutes 32.21 seconds (5312.21 seconds total)