Starting phenix.real_space_refine on Fri Sep 11 08:14:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wv2_66280/09_2026/9wv2_66280.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wv2_66280/09_2026/9wv2_66280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wv2_66280/09_2026/9wv2_66280.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wv2_66280/09_2026/9wv2_66280.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wv2_66280/09_2026/9wv2_66280.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wv2_66280/09_2026/9wv2_66280.map" } resolution = 3.15 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= 0.006 sd= 0.078 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 21 5.49 5 S 38 5.16 5 C 5461 2.51 5 N 1324 2.21 5 O 1516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8360 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 304 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "B" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 304 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "C" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 367 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "D" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 367 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "E" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 441 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "F" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 441 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "G" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 417 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "H" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 417 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "I" Number of atoms: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2189 Classifications: {'peptide': 286} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 272} Chain: "J" Number of atoms: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2189 Classifications: {'peptide': 286} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 272} Chain: "K" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 187 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 2, 'TRANS': 22} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 102 Unusual residues: {'PC1': 3, 'R16': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'PC1:plan-1': 1, 'PC1:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'PC1:plan-1': 1, 'PC1:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'PC1:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'PC1:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'PC1': 1, 'R16': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "I" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 118 Unusual residues: {'PC1': 4, 'R16': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 112 Planarities with less than four sites: {'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 208 Unusual residues: {'PC1': 5, 'R16': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 92 Time building chain proxies: 1.86, per 1000 atoms: 0.22 Number of scatterers: 8360 At special positions: 0 Unit cell: (93.1, 111.15, 133, 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 38 16.00 P 21 15.00 O 1516 8.00 N 1324 7.00 C 5461 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 439.3 milliseconds 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1768 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 2 sheets defined 35.1% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 13 through 46 removed outlier: 3.786A pdb=" N LYS A 17 " --> pdb=" O PRO A 13 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) Proline residue: A 42 - end of helix Processing helix chain 'B' and resid 14 through 47 Proline residue: B 42 - end of helix removed outlier: 3.723A pdb=" N LEU B 45 " --> pdb=" O THR B 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 40 through 61 Processing helix chain 'D' and resid 26 through 35 removed outlier: 4.179A pdb=" N GLY D 30 " --> pdb=" O ASP D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 62 removed outlier: 4.155A pdb=" N ILE D 46 " --> pdb=" O ARG D 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 25 Processing helix chain 'E' and resid 27 through 39 removed outlier: 3.613A pdb=" N GLY E 39 " --> pdb=" O GLY E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 53 Processing helix chain 'F' and resid 7 through 25 removed outlier: 4.564A pdb=" N ARG F 11 " --> pdb=" O GLU F 7 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE F 21 " --> pdb=" O LYS F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 38 Processing helix chain 'F' and resid 48 through 53 removed outlier: 3.608A pdb=" N LEU F 53 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 96 removed outlier: 3.818A pdb=" N ILE G 94 " --> pdb=" O THR G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 116 removed outlier: 4.242A pdb=" N GLN G 116 " --> pdb=" O GLN G 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 96 removed outlier: 3.577A pdb=" N LYS H 76 " --> pdb=" O PHE H 72 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU H 85 " --> pdb=" O SER H 81 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TRP H 86 " --> pdb=" O ARG H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 115 Processing helix chain 'I' and resid 82 through 89 removed outlier: 4.225A pdb=" N HIS I 87 " --> pdb=" O PHE I 83 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG I 88 " --> pdb=" O GLU I 84 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS I 89 " --> pdb=" O GLU I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 93 removed outlier: 3.719A pdb=" N LEU I 93 " --> pdb=" O CYS I 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 90 through 93' Processing helix chain 'J' and resid 82 through 92 removed outlier: 4.255A pdb=" N HIS J 87 " --> pdb=" O PHE J 83 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG J 88 " --> pdb=" O GLU J 84 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS J 89 " --> pdb=" O GLU J 85 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N CYS J 90 " --> pdb=" O CYS J 86 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS J 91 " --> pdb=" O HIS J 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 269 through 274 removed outlier: 3.925A pdb=" N LEU K 273 " --> pdb=" O LEU K 269 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU K 274 " --> pdb=" O THR K 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 269 through 274' Processing sheet with id=AA1, first strand: chain 'I' and resid 101 through 110 removed outlier: 3.643A pdb=" N LEU I 109 " --> pdb=" O PHE I 113 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY I 132 " --> pdb=" O ASN I 116 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS I 175 " --> pdb=" O ASP I 191 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA I 177 " --> pdb=" O GLN I 189 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN I 187 " --> pdb=" O GLN I 179 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL I 190 " --> pdb=" O LEU I 205 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA I 202 " --> pdb=" O HIS I 220 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU I 229 " --> pdb=" O ILE I 225 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY I 232 " --> pdb=" O ALA I 251 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA I 251 " --> pdb=" O GLY I 232 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU I 234 " --> pdb=" O SER I 249 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE I 323 " --> pdb=" O ASP I 319 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU I 332 " --> pdb=" O LEU I 337 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU I 337 " --> pdb=" O LEU I 332 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N LYS I 102 " --> pdb=" O LEU I 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 100 through 110 removed outlier: 6.637A pdb=" N PHE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU J 160 " --> pdb=" O THR J 180 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL J 190 " --> pdb=" O LEU J 205 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU J 222 " --> pdb=" O THR J 200 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA J 202 " --> pdb=" O HIS J 220 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY J 232 " --> pdb=" O ALA J 251 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA J 251 " --> pdb=" O GLY J 232 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP J 259 " --> pdb=" O LEU J 256 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR J 262 " --> pdb=" O THR J 273 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP J 296 " --> pdb=" O SER J 291 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE J 323 " --> pdb=" O ASP J 319 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLY J 100 " --> pdb=" O PHE J 356 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N LEU J 358 " --> pdb=" O GLY J 100 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LYS J 102 " --> pdb=" O LEU J 358 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ILE J 360 " --> pdb=" O LYS J 102 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR J 104 " --> pdb=" O ILE J 360 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1314 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.20 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1364 1.33 - 1.45: 2117 1.45 - 1.57: 4912 1.57 - 1.69: 42 1.69 - 1.82: 66 Bond restraints: 8501 Sorted by residual: bond pdb=" CG MET H 77 " pdb=" SD MET H 77 " ideal model delta sigma weight residual 1.803 1.778 0.025 2.50e-02 1.60e+03 9.66e-01 bond pdb=" CA THR J 264 " pdb=" C THR J 264 " ideal model delta sigma weight residual 1.523 1.538 -0.016 1.61e-02 3.86e+03 9.38e-01 bond pdb=" CA ASP I 306 " pdb=" CB ASP I 306 " ideal model delta sigma weight residual 1.534 1.553 -0.019 2.33e-02 1.84e+03 6.64e-01 bond pdb=" CA THR J 264 " pdb=" CB THR J 264 " ideal model delta sigma weight residual 1.526 1.539 -0.014 1.68e-02 3.54e+03 6.55e-01 bond pdb=" CA THR I 138 " pdb=" CB THR I 138 " ideal model delta sigma weight residual 1.527 1.546 -0.019 2.48e-02 1.63e+03 5.61e-01 ... (remaining 8496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 11280 2.19 - 4.39: 80 4.39 - 6.58: 16 6.58 - 8.78: 1 8.78 - 10.97: 3 Bond angle restraints: 11380 Sorted by residual: angle pdb=" CB PRO E 47 " pdb=" CG PRO E 47 " pdb=" CD PRO E 47 " ideal model delta sigma weight residual 106.10 95.16 10.94 3.20e+00 9.77e-02 1.17e+01 angle pdb=" CA LEU A 32 " pdb=" CB LEU A 32 " pdb=" CG LEU A 32 " ideal model delta sigma weight residual 116.30 127.27 -10.97 3.50e+00 8.16e-02 9.83e+00 angle pdb=" CA PRO E 47 " pdb=" CB PRO E 47 " pdb=" CG PRO E 47 " ideal model delta sigma weight residual 104.50 98.60 5.90 1.90e+00 2.77e-01 9.64e+00 angle pdb=" CA PRO E 47 " pdb=" N PRO E 47 " pdb=" CD PRO E 47 " ideal model delta sigma weight residual 112.00 107.70 4.30 1.40e+00 5.10e-01 9.44e+00 angle pdb=" CB MET H 77 " pdb=" CG MET H 77 " pdb=" SD MET H 77 " ideal model delta sigma weight residual 112.70 121.88 -9.18 3.00e+00 1.11e-01 9.37e+00 ... (remaining 11375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4219 17.93 - 35.86: 631 35.86 - 53.79: 279 53.79 - 71.72: 77 71.72 - 89.65: 19 Dihedral angle restraints: 5225 sinusoidal: 2473 harmonic: 2752 Sorted by residual: dihedral pdb=" CA ASP B 23 " pdb=" CB ASP B 23 " pdb=" CG ASP B 23 " pdb=" OD1 ASP B 23 " ideal model delta sinusoidal sigma weight residual -30.00 -85.19 55.19 1 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" CB GLU I 126 " pdb=" CG GLU I 126 " pdb=" CD GLU I 126 " pdb=" OE1 GLU I 126 " ideal model delta sinusoidal sigma weight residual 0.00 -87.96 87.96 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CG ARG J 239 " pdb=" CD ARG J 239 " pdb=" NE ARG J 239 " pdb=" CZ ARG J 239 " ideal model delta sinusoidal sigma weight residual 180.00 136.10 43.90 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 5222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1115 0.076 - 0.152: 85 0.152 - 0.228: 0 0.228 - 0.304: 0 0.304 - 0.380: 1 Chirality restraints: 1201 Sorted by residual: chirality pdb=" CG LEU A 32 " pdb=" CB LEU A 32 " pdb=" CD1 LEU A 32 " pdb=" CD2 LEU A 32 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CA VAL I 190 " pdb=" N VAL I 190 " pdb=" C VAL I 190 " pdb=" CB VAL I 190 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.01e-01 chirality pdb=" CA ILE D 65 " pdb=" N ILE D 65 " pdb=" C ILE D 65 " pdb=" CB ILE D 65 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 1198 not shown) Planarity restraints: 1368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR I 226 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO I 227 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO I 227 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO I 227 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR J 264 " -0.007 2.00e-02 2.50e+03 1.40e-02 1.97e+00 pdb=" C THR J 264 " 0.024 2.00e-02 2.50e+03 pdb=" O THR J 264 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU J 265 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR J 226 " 0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO J 227 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO J 227 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO J 227 " 0.018 5.00e-02 4.00e+02 ... (remaining 1365 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1259 2.77 - 3.30: 6896 3.30 - 3.83: 12199 3.83 - 4.37: 13601 4.37 - 4.90: 26597 Nonbonded interactions: 60552 Sorted by model distance: nonbonded pdb=" OE2 GLU H 104 " pdb=" OG1 THR K 270 " model vdw 2.232 3.040 nonbonded pdb=" OH TYR J 275 " pdb=" OE1 GLN J 283 " model vdw 2.242 3.040 nonbonded pdb=" OE2 GLU J 99 " pdb=" OG SER J 122 " model vdw 2.290 3.040 nonbonded pdb=" O THR J 138 " pdb=" OG1 THR J 138 " model vdw 2.292 3.040 nonbonded pdb=" OG SER I 159 " pdb=" O GLN I 181 " model vdw 2.308 3.040 ... (remaining 60547 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 13 through 48) } ncs_group { reference = (chain 'C' and (resid 25 through 69 or (resid 102 and (name C1 or name C2 or nam \ e O11 or name O12 or name O13 or name O14 or name O21 or name P )))) selection = (chain 'D' and (resid 25 through 69 or (resid 102 and (name C1 or name C2 or nam \ e O11 or name O12 or name O13 or name O14 or name O21 or name P )))) } ncs_group { reference = (chain 'E' and (resid 1 through 101 or (resid 102 and (name N or name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C3 or name C31 o \ r name C32 or name C33 or name O11 or name O12 or name O13 or name O14 or name O \ 21 or name O22 or name O31 or name O32 or name P )))) selection = (chain 'F' and (resid 1 through 101 or (resid 102 and (name N or name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C3 or name C31 o \ r name C32 or name C33 or name O11 or name O12 or name O13 or name O14 or name O \ 21 or name O22 or name O31 or name O32 or name P )))) } ncs_group { reference = (chain 'G' and resid 67 through 116) selection = (chain 'H' and resid 67 through 116) } ncs_group { reference = (chain 'I' and (resid 76 through 401 or (resid 402 and (name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 \ or name C40)) or resid 403 or (resid 404 and (name N or name C1 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 \ or name C23 or name C24 or name C3 or name C31 or name C32 or name C33 or name C \ 34 or name C35 or name C36 or name C37 or name C38 or name O11 or name O12 or na \ me O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P )) \ or (resid 405 and (name C1 or name C2 or name C21 or name C22 or name C3 or name \ C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name O11 or \ name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 \ or name P )))) selection = (chain 'J' and (resid 76 through 361 or (resid 401 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C3 or name C31 or name C32 or name C33 or name C34 \ or name C35 or name C36 or name C37 or name O11 or name O12 or name O13 or name \ O14 or name O21 or name O22 or name O31 or name O32 or name P )) or (resid 402 a \ nd (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name \ C37 or name C38 or name C39 or name C40)) or (resid 403 and (name N or name C1 \ or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C \ 3 or name C31 or name C32 or name C33 or name C34 or name O11 or name O12 or nam \ e O13 or name O14 or name O21 or name O31 or name O32 or name P )) or resid 404 \ or (resid 405 and (name C1 or name C2 or name C21 or name C22 or name C3 or name \ C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name O11 or \ name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 \ or name P )))) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.850 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 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 0.026 8501 Z= 0.100 Angle : 0.515 10.975 11380 Z= 0.259 Chirality : 0.040 0.380 1201 Planarity : 0.003 0.040 1368 Dihedral : 20.658 89.648 3457 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 33.70 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.30), residues: 947 helix: 2.68 (0.29), residues: 321 sheet: -0.62 (0.28), residues: 390 loop : -1.83 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 38 TYR 0.009 0.001 TYR A 34 PHE 0.019 0.001 PHE E 21 TRP 0.009 0.001 TRP J 259 HIS 0.003 0.001 HIS J 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 8501) covalent geometry : angle 0.51544 / 0.26 (11380) hydrogen bonds : bond 0.19126 / 12.89 ( 460) hydrogen bonds : angle 6.23953 / 4.46 ( 1314) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 176 MET cc_start: 0.7613 (mtm) cc_final: 0.7316 (mtm) REVERT: I 187 ASN cc_start: 0.8277 (t0) cc_final: 0.8055 (t0) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1025 time to fit residues: 14.0353 Evaluate side-chains 101 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.178436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.125093 restraints weight = 8567.866| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.71 r_work: 0.3311 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.0707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8501 Z= 0.124 Angle : 0.528 6.653 11380 Z= 0.272 Chirality : 0.040 0.281 1201 Planarity : 0.004 0.036 1368 Dihedral : 15.840 89.877 1642 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.55 % Allowed : 30.78 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.30), residues: 947 helix: 2.77 (0.29), residues: 322 sheet: -0.37 (0.28), residues: 400 loop : -1.73 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 38 TYR 0.009 0.001 TYR I 237 PHE 0.020 0.001 PHE B 43 TRP 0.007 0.001 TRP J 259 HIS 0.004 0.001 HIS J 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 8501) covalent geometry : angle 0.52845 / 0.27 (11380) hydrogen bonds : bond 0.04188 / 2.75 ( 460) hydrogen bonds : angle 4.11727 / 2.96 ( 1314) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 17 LYS cc_start: 0.7996 (mtmm) cc_final: 0.7736 (mtmm) REVERT: I 306 ASP cc_start: 0.8401 (p0) cc_final: 0.8198 (p0) REVERT: J 319 ASP cc_start: 0.8592 (t0) cc_final: 0.8221 (t0) outliers start: 21 outliers final: 11 residues processed: 112 average time/residue: 0.0900 time to fit residues: 13.9577 Evaluate side-chains 105 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain I residue 294 MET Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 306 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 63 optimal weight: 0.0670 chunk 68 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 7 optimal weight: 0.0870 chunk 58 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.180046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.127153 restraints weight = 8447.633| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.69 r_work: 0.3336 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8501 Z= 0.097 Angle : 0.489 6.407 11380 Z= 0.250 Chirality : 0.040 0.279 1201 Planarity : 0.003 0.035 1368 Dihedral : 14.856 87.888 1642 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.16 % Allowed : 30.17 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.30), residues: 947 helix: 2.99 (0.29), residues: 316 sheet: -0.05 (0.28), residues: 394 loop : -1.57 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 38 TYR 0.008 0.001 TYR I 194 PHE 0.014 0.001 PHE E 21 TRP 0.006 0.001 TRP J 259 HIS 0.002 0.001 HIS J 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 ( 8501) covalent geometry : angle 0.48944 / 0.25 (11380) hydrogen bonds : bond 0.03414 / 2.25 ( 460) hydrogen bonds : angle 3.80271 / 2.75 ( 1314) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 83 PHE cc_start: 0.7607 (OUTLIER) cc_final: 0.7024 (m-80) REVERT: J 91 LYS cc_start: 0.8482 (mmtt) cc_final: 0.8211 (mmtt) REVERT: J 223 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7173 (tp40) REVERT: J 319 ASP cc_start: 0.8563 (t0) cc_final: 0.8241 (t0) outliers start: 26 outliers final: 15 residues processed: 119 average time/residue: 0.0896 time to fit residues: 14.5831 Evaluate side-chains 113 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain I residue 83 PHE Chi-restraints excluded: chain I residue 87 HIS Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain I residue 294 MET Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 223 GLN Chi-restraints excluded: chain J residue 281 GLN Chi-restraints excluded: chain J residue 306 ASP Chi-restraints excluded: chain K residue 270 THR Chi-restraints excluded: chain K residue 280 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 3 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 38 optimal weight: 0.0870 chunk 89 optimal weight: 0.5980 chunk 7 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.179771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.128594 restraints weight = 8622.557| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.54 r_work: 0.3363 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8501 Z= 0.104 Angle : 0.492 6.772 11380 Z= 0.250 Chirality : 0.040 0.278 1201 Planarity : 0.003 0.035 1368 Dihedral : 14.501 89.987 1642 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.28 % Allowed : 30.05 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.30), residues: 947 helix: 3.01 (0.29), residues: 316 sheet: -0.00 (0.28), residues: 400 loop : -1.56 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 38 TYR 0.008 0.001 TYR I 237 PHE 0.011 0.001 PHE E 21 TRP 0.007 0.001 TRP J 259 HIS 0.003 0.001 HIS J 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 ( 8501) covalent geometry : angle 0.49236 / 0.25 (11380) hydrogen bonds : bond 0.03319 / 2.19 ( 460) hydrogen bonds : angle 3.66076 / 2.65 ( 1314) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 17 LYS cc_start: 0.7496 (mtmm) cc_final: 0.7291 (mtmm) REVERT: I 83 PHE cc_start: 0.7439 (OUTLIER) cc_final: 0.6838 (m-80) REVERT: I 187 ASN cc_start: 0.7721 (t0) cc_final: 0.7508 (t0) REVERT: J 91 LYS cc_start: 0.8308 (mmtt) cc_final: 0.8009 (mmtt) REVERT: J 223 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.6941 (tp40) REVERT: J 319 ASP cc_start: 0.8485 (t0) cc_final: 0.8110 (t0) outliers start: 27 outliers final: 15 residues processed: 121 average time/residue: 0.0904 time to fit residues: 14.8963 Evaluate side-chains 116 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain I residue 83 PHE Chi-restraints excluded: chain I residue 87 HIS Chi-restraints excluded: chain I residue 99 GLU Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain I residue 294 MET Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 223 GLN Chi-restraints excluded: chain J residue 281 GLN Chi-restraints excluded: chain J residue 306 ASP Chi-restraints excluded: chain K residue 270 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 52 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.177992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.126586 restraints weight = 8576.919| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.54 r_work: 0.3341 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8501 Z= 0.135 Angle : 0.528 7.331 11380 Z= 0.266 Chirality : 0.040 0.278 1201 Planarity : 0.003 0.036 1368 Dihedral : 14.584 88.459 1642 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.53 % Allowed : 30.66 % Favored : 65.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.30), residues: 947 helix: 2.97 (0.29), residues: 316 sheet: 0.06 (0.28), residues: 394 loop : -1.56 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 38 TYR 0.010 0.001 TYR I 237 PHE 0.012 0.001 PHE H 92 TRP 0.007 0.001 TRP J 188 HIS 0.004 0.001 HIS J 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 8501) covalent geometry : angle 0.52834 / 0.27 (11380) hydrogen bonds : bond 0.03666 / 2.41 ( 460) hydrogen bonds : angle 3.69934 / 2.68 ( 1314) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 PHE cc_start: 0.7930 (t80) cc_final: 0.7728 (t80) REVERT: I 83 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.6796 (m-80) REVERT: I 150 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7404 (mp) REVERT: I 305 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7868 (mp) REVERT: J 209 ASP cc_start: 0.7411 (t0) cc_final: 0.7204 (t0) REVERT: J 223 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.6920 (tp40) REVERT: J 319 ASP cc_start: 0.8460 (t0) cc_final: 0.8047 (t0) outliers start: 29 outliers final: 17 residues processed: 120 average time/residue: 0.0978 time to fit residues: 16.0667 Evaluate side-chains 117 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain I residue 83 PHE Chi-restraints excluded: chain I residue 99 GLU Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain I residue 294 MET Chi-restraints excluded: chain I residue 298 SER Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 223 GLN Chi-restraints excluded: chain J residue 281 GLN Chi-restraints excluded: chain J residue 306 ASP Chi-restraints excluded: chain K residue 270 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 78 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.177398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.126287 restraints weight = 8438.074| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.49 r_work: 0.3334 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8501 Z= 0.140 Angle : 0.542 8.505 11380 Z= 0.271 Chirality : 0.041 0.276 1201 Planarity : 0.003 0.036 1368 Dihedral : 14.579 86.099 1642 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.16 % Allowed : 30.78 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.30), residues: 947 helix: 2.96 (0.29), residues: 316 sheet: 0.05 (0.28), residues: 394 loop : -1.58 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 38 TYR 0.010 0.001 TYR I 237 PHE 0.012 0.001 PHE I 356 TRP 0.008 0.001 TRP J 259 HIS 0.004 0.001 HIS J 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 8501) covalent geometry : angle 0.54225 / 0.27 (11380) hydrogen bonds : bond 0.03720 / 2.45 ( 460) hydrogen bonds : angle 3.70686 / 2.69 ( 1314) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 PHE cc_start: 0.7893 (t80) cc_final: 0.7686 (t80) REVERT: I 83 PHE cc_start: 0.7424 (OUTLIER) cc_final: 0.6709 (m-80) REVERT: I 150 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7371 (mp) REVERT: I 305 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7830 (mp) REVERT: J 83 PHE cc_start: 0.6044 (OUTLIER) cc_final: 0.4949 (m-80) REVERT: J 209 ASP cc_start: 0.7400 (t0) cc_final: 0.7196 (t0) REVERT: J 223 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.6895 (tp40) REVERT: J 248 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8095 (ttt) REVERT: J 319 ASP cc_start: 0.8461 (t0) cc_final: 0.8033 (t0) outliers start: 26 outliers final: 17 residues processed: 117 average time/residue: 0.0920 time to fit residues: 14.6792 Evaluate side-chains 119 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain I residue 83 PHE Chi-restraints excluded: chain I residue 99 GLU Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain I residue 294 MET Chi-restraints excluded: chain I residue 298 SER Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 83 PHE Chi-restraints excluded: chain J residue 223 GLN Chi-restraints excluded: chain J residue 248 MET Chi-restraints excluded: chain J residue 281 GLN Chi-restraints excluded: chain J residue 306 ASP Chi-restraints excluded: chain K residue 270 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 0.0970 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.7978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.178770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.127431 restraints weight = 8601.604| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.54 r_work: 0.3349 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8501 Z= 0.114 Angle : 0.524 6.949 11380 Z= 0.262 Chirality : 0.040 0.272 1201 Planarity : 0.003 0.036 1368 Dihedral : 14.338 86.799 1642 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.04 % Allowed : 30.90 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.30), residues: 947 helix: 2.99 (0.29), residues: 316 sheet: 0.10 (0.28), residues: 394 loop : -1.54 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 38 TYR 0.009 0.001 TYR A 34 PHE 0.011 0.001 PHE H 92 TRP 0.009 0.001 TRP J 259 HIS 0.003 0.001 HIS J 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 ( 8501) covalent geometry : angle 0.52444 / 0.26 (11380) hydrogen bonds : bond 0.03400 / 2.24 ( 460) hydrogen bonds : angle 3.65023 / 2.66 ( 1314) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 PHE cc_start: 0.7884 (t80) cc_final: 0.7683 (t80) REVERT: I 83 PHE cc_start: 0.7456 (OUTLIER) cc_final: 0.6730 (m-80) REVERT: I 305 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7826 (mp) REVERT: J 83 PHE cc_start: 0.6107 (OUTLIER) cc_final: 0.5090 (m-80) REVERT: J 209 ASP cc_start: 0.7353 (t0) cc_final: 0.7146 (t0) REVERT: J 223 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.6913 (tp40) REVERT: J 248 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.7732 (tpt) REVERT: J 319 ASP cc_start: 0.8462 (t0) cc_final: 0.8070 (t0) outliers start: 25 outliers final: 18 residues processed: 118 average time/residue: 0.0991 time to fit residues: 16.0338 Evaluate side-chains 120 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain I residue 83 PHE Chi-restraints excluded: chain I residue 99 GLU Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain I residue 294 MET Chi-restraints excluded: chain I residue 298 SER Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 83 PHE Chi-restraints excluded: chain J residue 173 ARG Chi-restraints excluded: chain J residue 223 GLN Chi-restraints excluded: chain J residue 248 MET Chi-restraints excluded: chain J residue 281 GLN Chi-restraints excluded: chain J residue 306 ASP Chi-restraints excluded: chain K residue 270 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 3 optimal weight: 20.0000 chunk 77 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 87 optimal weight: 0.0570 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.179488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.128488 restraints weight = 8450.357| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.52 r_work: 0.3362 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8501 Z= 0.102 Angle : 0.520 9.993 11380 Z= 0.258 Chirality : 0.040 0.263 1201 Planarity : 0.003 0.036 1368 Dihedral : 14.078 89.722 1642 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.92 % Allowed : 31.39 % Favored : 65.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.30), residues: 947 helix: 3.12 (0.29), residues: 310 sheet: 0.16 (0.28), residues: 394 loop : -1.45 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 38 TYR 0.008 0.001 TYR A 34 PHE 0.011 0.001 PHE H 92 TRP 0.009 0.001 TRP J 259 HIS 0.003 0.001 HIS J 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 8501) covalent geometry : angle 0.51994 / 0.26 (11380) hydrogen bonds : bond 0.03194 / 2.11 ( 460) hydrogen bonds : angle 3.60939 / 2.64 ( 1314) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 PHE cc_start: 0.7922 (t80) cc_final: 0.7718 (t80) REVERT: I 83 PHE cc_start: 0.7552 (OUTLIER) cc_final: 0.6916 (m-80) REVERT: I 305 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7951 (mp) REVERT: J 223 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7008 (tp40) REVERT: J 319 ASP cc_start: 0.8456 (t0) cc_final: 0.8124 (t0) outliers start: 24 outliers final: 17 residues processed: 122 average time/residue: 0.0964 time to fit residues: 15.9887 Evaluate side-chains 120 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain I residue 83 PHE Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain I residue 294 MET Chi-restraints excluded: chain I residue 298 SER Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 173 ARG Chi-restraints excluded: chain J residue 223 GLN Chi-restraints excluded: chain J residue 281 GLN Chi-restraints excluded: chain J residue 306 ASP Chi-restraints excluded: chain K residue 270 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 29 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 18 optimal weight: 0.0370 chunk 60 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.179629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.128637 restraints weight = 8478.541| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.52 r_work: 0.3366 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8501 Z= 0.106 Angle : 0.528 8.953 11380 Z= 0.264 Chirality : 0.040 0.260 1201 Planarity : 0.003 0.036 1368 Dihedral : 13.974 88.518 1642 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.28 % Allowed : 31.51 % Favored : 65.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.30), residues: 947 helix: 3.07 (0.29), residues: 311 sheet: 0.19 (0.28), residues: 394 loop : -1.43 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 38 TYR 0.009 0.001 TYR A 34 PHE 0.012 0.001 PHE H 92 TRP 0.008 0.001 TRP J 259 HIS 0.003 0.001 HIS J 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 8501) covalent geometry : angle 0.52781 / 0.26 (11380) hydrogen bonds : bond 0.03223 / 2.13 ( 460) hydrogen bonds : angle 3.60729 / 2.64 ( 1314) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 83 PHE cc_start: 0.7428 (OUTLIER) cc_final: 0.6781 (m-80) REVERT: I 305 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7798 (mp) REVERT: J 83 PHE cc_start: 0.6111 (OUTLIER) cc_final: 0.5003 (m-80) REVERT: J 223 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.6940 (tp40) REVERT: J 319 ASP cc_start: 0.8430 (t0) cc_final: 0.8067 (t0) outliers start: 27 outliers final: 17 residues processed: 121 average time/residue: 0.0962 time to fit residues: 16.0571 Evaluate side-chains 120 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain I residue 83 PHE Chi-restraints excluded: chain I residue 99 GLU Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain I residue 294 MET Chi-restraints excluded: chain I residue 298 SER Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 83 PHE Chi-restraints excluded: chain J residue 173 ARG Chi-restraints excluded: chain J residue 223 GLN Chi-restraints excluded: chain J residue 281 GLN Chi-restraints excluded: chain J residue 306 ASP Chi-restraints excluded: chain K residue 270 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 65 optimal weight: 0.6980 chunk 14 optimal weight: 8.9990 chunk 61 optimal weight: 0.0170 chunk 76 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.178611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.127592 restraints weight = 8457.134| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.51 r_work: 0.3353 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8501 Z= 0.123 Angle : 0.548 9.909 11380 Z= 0.273 Chirality : 0.041 0.261 1201 Planarity : 0.003 0.036 1368 Dihedral : 14.061 88.156 1642 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.80 % Allowed : 32.00 % Favored : 65.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.30), residues: 947 helix: 3.04 (0.29), residues: 310 sheet: 0.16 (0.28), residues: 394 loop : -1.46 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 38 TYR 0.010 0.001 TYR A 34 PHE 0.017 0.001 PHE B 43 TRP 0.008 0.001 TRP J 259 HIS 0.004 0.001 HIS J 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 ( 8501) covalent geometry : angle 0.54784 / 0.27 (11380) hydrogen bonds : bond 0.03442 / 2.27 ( 460) hydrogen bonds : angle 3.64835 / 2.68 ( 1314) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 83 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.6722 (m-80) REVERT: I 150 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7409 (mp) REVERT: I 305 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7819 (mp) REVERT: J 83 PHE cc_start: 0.6150 (OUTLIER) cc_final: 0.5022 (m-80) REVERT: J 223 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.6960 (tp40) REVERT: J 319 ASP cc_start: 0.8431 (t0) cc_final: 0.8059 (t0) outliers start: 23 outliers final: 16 residues processed: 118 average time/residue: 0.0933 time to fit residues: 15.6889 Evaluate side-chains 120 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain I residue 83 PHE Chi-restraints excluded: chain I residue 99 GLU Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain I residue 294 MET Chi-restraints excluded: chain I residue 298 SER Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 83 PHE Chi-restraints excluded: chain J residue 173 ARG Chi-restraints excluded: chain J residue 223 GLN Chi-restraints excluded: chain J residue 281 GLN Chi-restraints excluded: chain J residue 306 ASP Chi-restraints excluded: chain K residue 270 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 42 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 47 optimal weight: 0.0060 chunk 28 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.176704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.125352 restraints weight = 8561.717| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.51 r_work: 0.3321 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8501 Z= 0.162 Angle : 0.580 8.303 11380 Z= 0.292 Chirality : 0.042 0.265 1201 Planarity : 0.003 0.036 1368 Dihedral : 14.449 88.682 1642 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.80 % Allowed : 32.24 % Favored : 64.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.30), residues: 947 helix: 2.83 (0.29), residues: 316 sheet: 0.06 (0.28), residues: 394 loop : -1.59 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 39 TYR 0.012 0.001 TYR A 34 PHE 0.013 0.001 PHE H 92 TRP 0.007 0.001 TRP J 188 HIS 0.004 0.001 HIS J 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.16 ( 8501) covalent geometry : angle 0.58006 / 0.29 (11380) hydrogen bonds : bond 0.03959 / 2.60 ( 460) hydrogen bonds : angle 3.76447 / 2.75 ( 1314) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1890.24 seconds wall clock time: 33 minutes 8.03 seconds (1988.03 seconds total)