Starting phenix.real_space_refine on Fri Feb 14 01:59:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7duq_30866/02_2025/7duq_30866_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7duq_30866/02_2025/7duq_30866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7duq_30866/02_2025/7duq_30866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7duq_30866/02_2025/7duq_30866.map" model { file = "/net/cci-nas-00/data/ceres_data/7duq_30866/02_2025/7duq_30866_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7duq_30866/02_2025/7duq_30866_trim.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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 S 55 5.16 5 Cl 2 4.86 5 C 6175 2.51 5 N 1632 2.21 5 O 1738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9602 Number of models: 1 Model: "" Number of chains: 7 Chain: "P" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 233 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "R" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3176 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 14, 'TRANS': 369} Chain breaks: 2 Chain: "A" Number of atoms: 1990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1990 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 2 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 213 Unusual residues: {'CLR': 7, 'HNO': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 5.54, per 1000 atoms: 0.58 Number of scatterers: 9602 At special positions: 0 Unit cell: (164.065, 105.545, 97.185, 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) Cl 2 17.00 S 55 16.00 O 1738 8.00 N 1632 7.00 C 6175 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.04 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.1 seconds 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2212 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 42.8% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'P' and resid 7 through 35 Processing helix chain 'R' and resid 31 through 53 Processing helix chain 'R' and resid 137 through 169 removed outlier: 3.653A pdb=" N PHE R 143 " --> pdb=" O GLU R 139 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER R 157 " --> pdb=" O ALA R 153 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 173 Processing helix chain 'R' and resid 174 through 205 Processing helix chain 'R' and resid 206 through 215 Processing helix chain 'R' and resid 223 through 256 removed outlier: 3.628A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE R 230 " --> pdb=" O CYS R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 275 Processing helix chain 'R' and resid 277 through 292 removed outlier: 3.580A pdb=" N VAL R 282 " --> pdb=" O LEU R 278 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 302 through 338 removed outlier: 3.692A pdb=" N ILE R 308 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 345 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 366 Processing helix chain 'R' and resid 376 through 393 Processing helix chain 'R' and resid 393 through 403 Processing helix chain 'R' and resid 406 through 422 Processing helix chain 'A' and resid 12 through 39 Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 52 through 63 removed outlier: 3.592A pdb=" N LEU A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 293 through 303 removed outlier: 4.100A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.902A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.578A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.512A pdb=" N PHE A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.860A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.570A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'R' and resid 65 through 66 removed outlier: 3.894A pdb=" N THR R 65 " --> pdb=" O TRP R 72 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TRP R 72 " --> pdb=" O THR R 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'R' and resid 80 through 84 removed outlier: 3.632A pdb=" N TYR R 101 " --> pdb=" O ASP R 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.474A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.102A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.540A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.528A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.141A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.512A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.911A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.515A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.378A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.970A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 491 hydrogen bonds defined for protein. 1401 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: 2.84 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3039 1.34 - 1.46: 2354 1.46 - 1.58: 4366 1.58 - 1.71: 0 1.71 - 1.83: 76 Bond restraints: 9835 Sorted by residual: bond pdb=" C14 HNO R 501 " pdb=" N15 HNO R 501 " ideal model delta sigma weight residual 1.348 1.457 -0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C20 HNO R 501 " pdb=" C21 HNO R 501 " ideal model delta sigma weight residual 1.418 1.357 0.061 2.00e-02 2.50e+03 9.43e+00 bond pdb=" C12 HNO R 501 " pdb=" C14 HNO R 501 " ideal model delta sigma weight residual 1.450 1.399 0.051 2.00e-02 2.50e+03 6.62e+00 bond pdb=" C24 HNO R 501 " pdb="CL2 HNO R 501 " ideal model delta sigma weight residual 1.740 1.784 -0.044 2.00e-02 2.50e+03 4.95e+00 bond pdb=" C23 HNO R 501 " pdb="CL1 HNO R 501 " ideal model delta sigma weight residual 1.741 1.785 -0.044 2.00e-02 2.50e+03 4.94e+00 ... (remaining 9830 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 13007 2.14 - 4.28: 308 4.28 - 6.42: 43 6.42 - 8.55: 12 8.55 - 10.69: 2 Bond angle restraints: 13372 Sorted by residual: angle pdb=" CA TYR R 148 " pdb=" CB TYR R 148 " pdb=" CG TYR R 148 " ideal model delta sigma weight residual 113.90 122.27 -8.37 1.80e+00 3.09e-01 2.16e+01 angle pdb=" C GLY R 275 " pdb=" N VAL R 276 " pdb=" CA VAL R 276 " ideal model delta sigma weight residual 120.24 123.02 -2.78 6.30e-01 2.52e+00 1.95e+01 angle pdb=" CB MET B 61 " pdb=" CG MET B 61 " pdb=" SD MET B 61 " ideal model delta sigma weight residual 112.70 102.01 10.69 3.00e+00 1.11e-01 1.27e+01 angle pdb=" N VAL R 259 " pdb=" CA VAL R 259 " pdb=" C VAL R 259 " ideal model delta sigma weight residual 106.85 111.78 -4.93 1.42e+00 4.96e-01 1.21e+01 angle pdb=" C VAL N 48 " pdb=" N SER N 49 " pdb=" CA SER N 49 " ideal model delta sigma weight residual 121.64 115.96 5.68 1.70e+00 3.46e-01 1.12e+01 ... (remaining 13367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.59: 5873 24.59 - 49.18: 227 49.18 - 73.77: 36 73.77 - 98.35: 8 98.35 - 122.94: 3 Dihedral angle restraints: 6147 sinusoidal: 2726 harmonic: 3421 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -24.13 -61.87 1 1.00e+01 1.00e-02 5.07e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -146.08 -33.92 0 5.00e+00 4.00e-02 4.60e+01 dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 -144.37 58.37 1 1.00e+01 1.00e-02 4.56e+01 ... (remaining 6144 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1309 0.077 - 0.154: 157 0.154 - 0.231: 10 0.231 - 0.308: 8 0.308 - 0.385: 6 Chirality restraints: 1490 Sorted by residual: chirality pdb=" C14 CLR R 506 " pdb=" C13 CLR R 506 " pdb=" C15 CLR R 506 " pdb=" C8 CLR R 506 " both_signs ideal model delta sigma weight residual False -2.32 -2.70 0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" C14 CLR R 508 " pdb=" C13 CLR R 508 " pdb=" C15 CLR R 508 " pdb=" C8 CLR R 508 " both_signs ideal model delta sigma weight residual False -2.32 -2.70 0.38 2.00e-01 2.50e+01 3.64e+00 chirality pdb=" C14 CLR R 505 " pdb=" C13 CLR R 505 " pdb=" C15 CLR R 505 " pdb=" C8 CLR R 505 " both_signs ideal model delta sigma weight residual False -2.32 -2.67 0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 1487 not shown) Planarity restraints: 1658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 357 " 0.023 2.00e-02 2.50e+03 2.77e-02 1.15e+01 pdb=" CG HIS A 357 " -0.058 2.00e-02 2.50e+03 pdb=" ND1 HIS A 357 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 HIS A 357 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 HIS A 357 " -0.009 2.00e-02 2.50e+03 pdb=" NE2 HIS A 357 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 148 " -0.032 2.00e-02 2.50e+03 2.20e-02 9.66e+00 pdb=" CG TYR R 148 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR R 148 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR R 148 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR R 148 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR R 148 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR R 148 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR R 148 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 234 " -0.008 2.00e-02 2.50e+03 1.66e-02 4.83e+00 pdb=" CG PHE B 234 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE B 234 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE B 234 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE B 234 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE B 234 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 234 " -0.003 2.00e-02 2.50e+03 ... (remaining 1655 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 214 2.68 - 3.24: 9533 3.24 - 3.79: 16344 3.79 - 4.35: 22538 4.35 - 4.90: 36126 Nonbonded interactions: 84755 Sorted by model distance: nonbonded pdb=" OE2 GLU P 9 " pdb=" OH TYR R 152 " model vdw 2.126 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.140 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.157 3.040 nonbonded pdb=" OH TYR A 253 " pdb=" O LYS A 307 " model vdw 2.180 3.040 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.186 3.040 ... (remaining 84750 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 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 23.860 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 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 : 0.006 0.109 9835 Z= 0.413 Angle : 0.819 10.693 13372 Z= 0.443 Chirality : 0.058 0.385 1490 Planarity : 0.005 0.045 1658 Dihedral : 13.618 122.944 3917 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.30 % Allowed : 2.67 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.23), residues: 1154 helix: -0.60 (0.22), residues: 454 sheet: -0.48 (0.29), residues: 265 loop : -0.31 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.032 0.003 HIS A 357 PHE 0.034 0.003 PHE B 234 TYR 0.052 0.002 TYR R 148 ARG 0.006 0.001 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 192 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: R 265 ILE cc_start: 0.7346 (tp) cc_final: 0.7087 (tp) REVERT: R 293 ASP cc_start: 0.6091 (p0) cc_final: 0.5821 (p0) REVERT: A 299 GLU cc_start: 0.5918 (mt-10) cc_final: 0.5600 (tp30) REVERT: B 176 GLN cc_start: 0.8410 (tt0) cc_final: 0.8119 (tt0) REVERT: B 188 MET cc_start: 0.8517 (mmm) cc_final: 0.8235 (mmm) REVERT: B 220 GLN cc_start: 0.7838 (mt0) cc_final: 0.7214 (mt0) REVERT: B 273 ILE cc_start: 0.8114 (mt) cc_final: 0.7902 (mp) REVERT: G 21 MET cc_start: 0.4481 (ptp) cc_final: 0.3995 (pmm) outliers start: 3 outliers final: 3 residues processed: 193 average time/residue: 1.3969 time to fit residues: 286.8171 Evaluate side-chains 150 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 147 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 59 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 104 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 177 ASN R 180 HIS R 221 GLN R 302 ASN R 363 HIS A 14 ASN A 262 GLN A 278 ASN A 387 HIS B 155 ASN B 176 GLN B 268 ASN N 5 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.199481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.143596 restraints weight = 9986.852| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.21 r_work: 0.3658 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9835 Z= 0.215 Angle : 0.591 8.033 13372 Z= 0.310 Chirality : 0.043 0.179 1490 Planarity : 0.004 0.043 1658 Dihedral : 7.943 59.776 1749 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.27 % Allowed : 9.87 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.24), residues: 1154 helix: 0.94 (0.23), residues: 448 sheet: -0.36 (0.29), residues: 250 loop : -0.07 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 243 HIS 0.006 0.001 HIS R 180 PHE 0.017 0.002 PHE R 230 TYR 0.033 0.002 TYR R 148 ARG 0.010 0.001 ARG R 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 40 ARG cc_start: 0.7871 (ttm-80) cc_final: 0.7662 (ttm-80) REVERT: R 126 CYS cc_start: 0.5332 (m) cc_final: 0.5086 (m) REVERT: R 265 ILE cc_start: 0.6955 (tp) cc_final: 0.6678 (tp) REVERT: R 293 ASP cc_start: 0.7446 (p0) cc_final: 0.7199 (p0) REVERT: R 414 ARG cc_start: 0.6981 (ttp-110) cc_final: 0.6747 (ttm110) REVERT: R 417 TRP cc_start: 0.7231 (t-100) cc_final: 0.7000 (t-100) REVERT: A 28 LYS cc_start: 0.7379 (mttt) cc_final: 0.6412 (pttp) REVERT: B 96 ARG cc_start: 0.8669 (mtp85) cc_final: 0.7771 (mpp-170) REVERT: B 176 GLN cc_start: 0.8958 (tt0) cc_final: 0.8665 (tt0) REVERT: B 214 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.7236 (mmp80) REVERT: B 217 MET cc_start: 0.7372 (mmm) cc_final: 0.6565 (ptm) REVERT: G 21 MET cc_start: 0.3758 (ptp) cc_final: 0.3228 (pmm) REVERT: N 5 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7179 (tm-30) REVERT: N 35 ASN cc_start: 0.8158 (OUTLIER) cc_final: 0.7689 (m-40) REVERT: N 103 PHE cc_start: 0.7892 (m-80) cc_final: 0.7520 (m-80) REVERT: N 120 GLN cc_start: 0.8098 (mm110) cc_final: 0.7673 (mm110) outliers start: 23 outliers final: 7 residues processed: 175 average time/residue: 1.3196 time to fit residues: 246.4133 Evaluate side-chains 148 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 47 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 407 ASN A 267 GLN B 268 ASN N 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.197973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.141240 restraints weight = 10193.211| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.24 r_work: 0.3634 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9835 Z= 0.255 Angle : 0.562 8.750 13372 Z= 0.299 Chirality : 0.043 0.173 1490 Planarity : 0.004 0.041 1658 Dihedral : 7.471 59.816 1747 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.07 % Allowed : 13.52 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.25), residues: 1154 helix: 1.40 (0.24), residues: 447 sheet: -0.46 (0.30), residues: 252 loop : 0.07 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 243 HIS 0.007 0.001 HIS A 357 PHE 0.020 0.002 PHE R 230 TYR 0.036 0.002 TYR R 148 ARG 0.007 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 41 GLU cc_start: 0.7149 (tp30) cc_final: 0.6842 (tp30) REVERT: R 265 ILE cc_start: 0.7056 (tp) cc_final: 0.6833 (tp) REVERT: R 293 ASP cc_start: 0.7276 (p0) cc_final: 0.6993 (p0) REVERT: R 417 TRP cc_start: 0.7221 (t-100) cc_final: 0.6973 (t-100) REVERT: A 20 ARG cc_start: 0.6945 (mtp85) cc_final: 0.6207 (mtm-85) REVERT: A 28 LYS cc_start: 0.7434 (mttt) cc_final: 0.6454 (pttp) REVERT: A 283 ARG cc_start: 0.7193 (mtm110) cc_final: 0.6375 (mmt180) REVERT: B 214 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.6957 (mmp80) REVERT: B 217 MET cc_start: 0.7756 (mmm) cc_final: 0.6966 (ppp) REVERT: G 21 MET cc_start: 0.3768 (ptp) cc_final: 0.3261 (pmm) REVERT: N 5 GLN cc_start: 0.7769 (tt0) cc_final: 0.7288 (tm-30) REVERT: N 35 ASN cc_start: 0.8262 (OUTLIER) cc_final: 0.7967 (m-40) outliers start: 21 outliers final: 7 residues processed: 154 average time/residue: 1.3127 time to fit residues: 216.0092 Evaluate side-chains 143 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 40 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 44 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 263 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.197148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.140191 restraints weight = 10018.264| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.24 r_work: 0.3608 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9835 Z= 0.248 Angle : 0.551 8.609 13372 Z= 0.292 Chirality : 0.042 0.173 1490 Planarity : 0.004 0.068 1658 Dihedral : 7.309 57.600 1747 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.96 % Allowed : 13.72 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.25), residues: 1154 helix: 1.67 (0.24), residues: 445 sheet: -0.43 (0.30), residues: 252 loop : 0.09 (0.32), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 39 HIS 0.007 0.001 HIS A 357 PHE 0.018 0.002 PHE R 230 TYR 0.036 0.002 TYR R 148 ARG 0.014 0.001 ARG R 414 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 40 ARG cc_start: 0.8000 (ttm-80) cc_final: 0.7792 (ttm-80) REVERT: R 41 GLU cc_start: 0.7250 (tp30) cc_final: 0.6881 (tp30) REVERT: R 265 ILE cc_start: 0.7044 (tp) cc_final: 0.6824 (tp) REVERT: R 293 ASP cc_start: 0.7292 (p0) cc_final: 0.7020 (p0) REVERT: R 353 THR cc_start: 0.8756 (m) cc_final: 0.8157 (p) REVERT: R 414 ARG cc_start: 0.7023 (ttm110) cc_final: 0.6701 (ttm170) REVERT: R 417 TRP cc_start: 0.7199 (t-100) cc_final: 0.6953 (t-100) REVERT: A 20 ARG cc_start: 0.6781 (mtp85) cc_final: 0.6034 (mtm-85) REVERT: A 21 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6747 (pt0) REVERT: A 28 LYS cc_start: 0.7422 (mttt) cc_final: 0.6400 (pttp) REVERT: B 214 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.7120 (mmp80) REVERT: B 217 MET cc_start: 0.7697 (mmm) cc_final: 0.7097 (ppp) REVERT: G 21 MET cc_start: 0.3710 (ptp) cc_final: 0.3270 (pmm) REVERT: N 5 GLN cc_start: 0.7692 (tt0) cc_final: 0.7134 (tm-30) REVERT: N 35 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.7938 (m-40) outliers start: 30 outliers final: 12 residues processed: 156 average time/residue: 1.2908 time to fit residues: 216.1879 Evaluate side-chains 147 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 95 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 64 optimal weight: 0.2980 chunk 114 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 263 GLN R 374 HIS B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.199176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.142942 restraints weight = 10068.184| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.24 r_work: 0.3646 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9835 Z= 0.187 Angle : 0.512 8.360 13372 Z= 0.272 Chirality : 0.041 0.173 1490 Planarity : 0.004 0.041 1658 Dihedral : 6.883 56.012 1747 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.16 % Allowed : 14.41 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.25), residues: 1154 helix: 1.98 (0.24), residues: 443 sheet: -0.37 (0.31), residues: 250 loop : 0.13 (0.32), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 39 HIS 0.005 0.001 HIS A 357 PHE 0.019 0.001 PHE R 143 TYR 0.034 0.002 TYR R 148 ARG 0.010 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 ARG cc_start: 0.7990 (ttm-80) cc_final: 0.7723 (ttm-80) REVERT: R 41 GLU cc_start: 0.7308 (tp30) cc_final: 0.6967 (tp30) REVERT: R 265 ILE cc_start: 0.7201 (tp) cc_final: 0.6933 (tp) REVERT: R 293 ASP cc_start: 0.7223 (p0) cc_final: 0.6880 (p0) REVERT: R 353 THR cc_start: 0.8751 (m) cc_final: 0.8413 (m) REVERT: A 20 ARG cc_start: 0.6767 (mtp85) cc_final: 0.6021 (mtm-85) REVERT: A 21 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6799 (pt0) REVERT: A 28 LYS cc_start: 0.7409 (mttt) cc_final: 0.6387 (pttp) REVERT: A 210 THR cc_start: 0.6894 (p) cc_final: 0.6597 (t) REVERT: A 283 ARG cc_start: 0.7176 (mtm110) cc_final: 0.6410 (mmt180) REVERT: B 214 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.7057 (mmp80) REVERT: B 217 MET cc_start: 0.7657 (mmm) cc_final: 0.7237 (ppp) REVERT: B 252 LEU cc_start: 0.8575 (tt) cc_final: 0.8306 (tp) REVERT: N 5 GLN cc_start: 0.7616 (tt0) cc_final: 0.7140 (tm-30) REVERT: N 35 ASN cc_start: 0.8133 (OUTLIER) cc_final: 0.7887 (m-40) outliers start: 32 outliers final: 15 residues processed: 173 average time/residue: 1.1902 time to fit residues: 221.6298 Evaluate side-chains 155 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 81 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 212 HIS R 263 GLN B 176 GLN B 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.198207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.141774 restraints weight = 10102.990| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.25 r_work: 0.3631 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9835 Z= 0.221 Angle : 0.539 10.436 13372 Z= 0.283 Chirality : 0.042 0.214 1490 Planarity : 0.004 0.065 1658 Dihedral : 6.877 58.990 1747 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.67 % Allowed : 15.89 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.25), residues: 1154 helix: 1.96 (0.24), residues: 445 sheet: -0.32 (0.31), residues: 250 loop : 0.07 (0.32), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 264 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.001 PHE R 230 TYR 0.031 0.002 TYR R 148 ARG 0.014 0.001 ARG R 414 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 9 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7614 (tp30) REVERT: R 41 GLU cc_start: 0.7347 (tp30) cc_final: 0.6976 (tp30) REVERT: R 211 GLN cc_start: 0.7463 (mm-40) cc_final: 0.7083 (tp-100) REVERT: R 293 ASP cc_start: 0.7222 (p0) cc_final: 0.6885 (p0) REVERT: R 353 THR cc_start: 0.8737 (m) cc_final: 0.8378 (m) REVERT: A 20 ARG cc_start: 0.6770 (mtp85) cc_final: 0.6019 (mtm-85) REVERT: A 21 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6790 (pt0) REVERT: A 28 LYS cc_start: 0.7341 (mttt) cc_final: 0.6331 (pttp) REVERT: A 210 THR cc_start: 0.6798 (p) cc_final: 0.6505 (t) REVERT: B 96 ARG cc_start: 0.8581 (mtp85) cc_final: 0.7804 (mmt180) REVERT: B 214 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6988 (mmp80) REVERT: B 217 MET cc_start: 0.7444 (mmm) cc_final: 0.7046 (ppp) REVERT: B 252 LEU cc_start: 0.8613 (tt) cc_final: 0.8336 (tp) REVERT: G 21 MET cc_start: 0.3863 (ptp) cc_final: 0.3302 (pmm) REVERT: N 5 GLN cc_start: 0.7600 (tt0) cc_final: 0.7137 (tm-30) REVERT: N 114 THR cc_start: 0.7919 (p) cc_final: 0.7527 (m) outliers start: 27 outliers final: 17 residues processed: 163 average time/residue: 1.1942 time to fit residues: 209.0930 Evaluate side-chains 161 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 GLU Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 90 optimal weight: 0.4980 chunk 111 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 212 HIS R 263 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.198295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.141871 restraints weight = 10121.305| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.24 r_work: 0.3635 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9835 Z= 0.207 Angle : 0.530 9.773 13372 Z= 0.278 Chirality : 0.041 0.154 1490 Planarity : 0.004 0.039 1658 Dihedral : 6.757 58.677 1747 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.26 % Allowed : 15.99 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.25), residues: 1154 helix: 2.08 (0.24), residues: 443 sheet: -0.28 (0.32), residues: 250 loop : 0.06 (0.31), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 264 HIS 0.005 0.001 HIS A 357 PHE 0.017 0.001 PHE R 230 TYR 0.030 0.002 TYR R 148 ARG 0.013 0.001 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 41 GLU cc_start: 0.7361 (tp30) cc_final: 0.7018 (tp30) REVERT: R 211 GLN cc_start: 0.7461 (mm-40) cc_final: 0.7047 (tp-100) REVERT: R 293 ASP cc_start: 0.7234 (p0) cc_final: 0.6900 (p0) REVERT: R 414 ARG cc_start: 0.7065 (ttm110) cc_final: 0.6653 (ttm110) REVERT: A 20 ARG cc_start: 0.6754 (mtp85) cc_final: 0.6005 (mtm-85) REVERT: A 21 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6773 (pt0) REVERT: A 28 LYS cc_start: 0.7354 (mttt) cc_final: 0.6347 (pttp) REVERT: A 210 THR cc_start: 0.6800 (p) cc_final: 0.6521 (t) REVERT: A 283 ARG cc_start: 0.7235 (mtm110) cc_final: 0.6385 (mmt180) REVERT: A 372 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8180 (mp) REVERT: B 96 ARG cc_start: 0.8616 (mtp85) cc_final: 0.7805 (mmt180) REVERT: B 214 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.7114 (mmp80) REVERT: B 217 MET cc_start: 0.7378 (mmm) cc_final: 0.7097 (ppp) REVERT: B 252 LEU cc_start: 0.8589 (tt) cc_final: 0.8277 (tp) REVERT: B 258 ASP cc_start: 0.6036 (OUTLIER) cc_final: 0.5427 (m-30) REVERT: G 21 MET cc_start: 0.3776 (ptp) cc_final: 0.3276 (pmm) REVERT: G 50 LEU cc_start: 0.7605 (mt) cc_final: 0.6999 (mp) REVERT: N 5 GLN cc_start: 0.7599 (tt0) cc_final: 0.7088 (tm-30) REVERT: N 114 THR cc_start: 0.7904 (p) cc_final: 0.7514 (m) outliers start: 33 outliers final: 16 residues processed: 166 average time/residue: 1.2041 time to fit residues: 214.8456 Evaluate side-chains 155 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 6 optimal weight: 8.9990 chunk 46 optimal weight: 0.0870 chunk 91 optimal weight: 0.0170 chunk 44 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 212 HIS R 263 GLN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.197740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.141097 restraints weight = 10137.112| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.25 r_work: 0.3623 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9835 Z= 0.227 Angle : 0.546 9.328 13372 Z= 0.286 Chirality : 0.042 0.198 1490 Planarity : 0.004 0.039 1658 Dihedral : 6.610 55.534 1745 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.67 % Allowed : 17.28 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.25), residues: 1154 helix: 1.95 (0.23), residues: 452 sheet: -0.30 (0.32), residues: 250 loop : -0.00 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 264 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.001 PHE R 230 TYR 0.027 0.002 TYR R 148 ARG 0.011 0.000 ARG R 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 1.091 Fit side-chains revert: symmetry clash REVERT: R 40 ARG cc_start: 0.7920 (ttm-80) cc_final: 0.7202 (mtp180) REVERT: R 41 GLU cc_start: 0.7351 (tp30) cc_final: 0.7032 (tp30) REVERT: R 211 GLN cc_start: 0.7472 (mm-40) cc_final: 0.7047 (tp-100) REVERT: R 293 ASP cc_start: 0.7162 (p0) cc_final: 0.6835 (p0) REVERT: A 20 ARG cc_start: 0.6749 (mtp85) cc_final: 0.6031 (mtm-85) REVERT: A 21 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6762 (pt0) REVERT: A 28 LYS cc_start: 0.7333 (mttt) cc_final: 0.6326 (pttp) REVERT: A 210 THR cc_start: 0.6841 (p) cc_final: 0.6564 (t) REVERT: A 283 ARG cc_start: 0.7265 (mtm110) cc_final: 0.6396 (mmt180) REVERT: A 372 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8182 (mp) REVERT: B 96 ARG cc_start: 0.8590 (mtp85) cc_final: 0.7807 (mmt180) REVERT: B 214 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.7119 (mmp80) REVERT: B 217 MET cc_start: 0.7383 (mmm) cc_final: 0.7100 (ppp) REVERT: B 252 LEU cc_start: 0.8595 (tt) cc_final: 0.8305 (tp) REVERT: B 258 ASP cc_start: 0.5939 (OUTLIER) cc_final: 0.5590 (m-30) REVERT: G 21 MET cc_start: 0.3747 (ptp) cc_final: 0.3265 (pmm) REVERT: G 50 LEU cc_start: 0.7753 (mt) cc_final: 0.7166 (mp) REVERT: N 5 GLN cc_start: 0.7608 (tt0) cc_final: 0.7094 (tm-30) REVERT: N 114 THR cc_start: 0.7943 (p) cc_final: 0.7550 (m) outliers start: 27 outliers final: 17 residues processed: 158 average time/residue: 1.1972 time to fit residues: 203.1531 Evaluate side-chains 152 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 15 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 212 HIS R 263 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.198025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.141528 restraints weight = 10105.635| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.25 r_work: 0.3630 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9835 Z= 0.216 Angle : 0.543 9.190 13372 Z= 0.284 Chirality : 0.042 0.219 1490 Planarity : 0.004 0.038 1658 Dihedral : 6.521 55.693 1745 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.47 % Allowed : 17.87 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.25), residues: 1154 helix: 2.06 (0.24), residues: 444 sheet: -0.28 (0.32), residues: 250 loop : 0.04 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP R 264 HIS 0.006 0.001 HIS A 357 PHE 0.017 0.001 PHE R 230 TYR 0.015 0.002 TYR R 205 ARG 0.010 0.000 ARG R 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 41 GLU cc_start: 0.7347 (tp30) cc_final: 0.7043 (tp30) REVERT: R 293 ASP cc_start: 0.7156 (p0) cc_final: 0.6841 (p0) REVERT: A 20 ARG cc_start: 0.6732 (mtp85) cc_final: 0.6020 (mtm-85) REVERT: A 21 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6758 (pt0) REVERT: A 28 LYS cc_start: 0.7352 (mttt) cc_final: 0.6347 (pttp) REVERT: A 210 THR cc_start: 0.6865 (p) cc_final: 0.6591 (t) REVERT: A 372 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8168 (mp) REVERT: B 96 ARG cc_start: 0.8579 (mtp85) cc_final: 0.7820 (mmt180) REVERT: B 214 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.7126 (mmp80) REVERT: B 252 LEU cc_start: 0.8589 (tt) cc_final: 0.8297 (tp) REVERT: G 21 MET cc_start: 0.3700 (ptp) cc_final: 0.3235 (pmm) REVERT: N 5 GLN cc_start: 0.7579 (tt0) cc_final: 0.7082 (tm-30) REVERT: N 114 THR cc_start: 0.8011 (p) cc_final: 0.7597 (m) outliers start: 25 outliers final: 18 residues processed: 157 average time/residue: 1.2293 time to fit residues: 208.0317 Evaluate side-chains 154 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 13 optimal weight: 0.0980 chunk 5 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 113 optimal weight: 0.8980 chunk 11 optimal weight: 20.0000 chunk 26 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 212 HIS R 263 GLN A 278 ASN B 156 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.199413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.143046 restraints weight = 10123.823| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.25 r_work: 0.3647 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9835 Z= 0.187 Angle : 0.535 9.135 13372 Z= 0.279 Chirality : 0.042 0.210 1490 Planarity : 0.004 0.053 1658 Dihedral : 6.399 56.421 1745 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.27 % Allowed : 18.66 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.25), residues: 1154 helix: 2.16 (0.24), residues: 444 sheet: -0.26 (0.32), residues: 250 loop : 0.05 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP R 264 HIS 0.006 0.001 HIS R 212 PHE 0.016 0.001 PHE R 143 TYR 0.014 0.002 TYR R 205 ARG 0.013 0.001 ARG A 283 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: R 40 ARG cc_start: 0.7927 (ttm-80) cc_final: 0.7277 (mtp180) REVERT: R 293 ASP cc_start: 0.7140 (p0) cc_final: 0.6812 (p0) REVERT: A 20 ARG cc_start: 0.6727 (mtp85) cc_final: 0.5981 (mtm-85) REVERT: A 21 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6746 (pt0) REVERT: A 28 LYS cc_start: 0.7335 (mttt) cc_final: 0.6333 (pttp) REVERT: A 210 THR cc_start: 0.6861 (p) cc_final: 0.6592 (t) REVERT: A 278 ASN cc_start: 0.8578 (m-40) cc_final: 0.8313 (m-40) REVERT: A 283 ARG cc_start: 0.7273 (mtm110) cc_final: 0.6398 (mmt180) REVERT: A 372 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8155 (mp) REVERT: A 389 ARG cc_start: 0.7808 (ttp-110) cc_final: 0.7555 (mtm110) REVERT: B 96 ARG cc_start: 0.8563 (mtp85) cc_final: 0.7809 (mmt180) REVERT: B 252 LEU cc_start: 0.8491 (tt) cc_final: 0.8182 (tp) REVERT: G 21 MET cc_start: 0.3755 (ptp) cc_final: 0.3273 (pmm) REVERT: G 50 LEU cc_start: 0.7656 (mt) cc_final: 0.7054 (mp) REVERT: N 5 GLN cc_start: 0.7580 (tt0) cc_final: 0.7087 (tm-30) REVERT: N 114 THR cc_start: 0.8003 (p) cc_final: 0.7726 (t) outliers start: 23 outliers final: 16 residues processed: 153 average time/residue: 1.1999 time to fit residues: 197.4875 Evaluate side-chains 152 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 15 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 0.0870 chunk 50 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 84 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 212 HIS R 263 GLN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.198326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.141706 restraints weight = 10068.307| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.23 r_work: 0.3631 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9835 Z= 0.223 Angle : 0.549 9.051 13372 Z= 0.287 Chirality : 0.043 0.262 1490 Planarity : 0.004 0.055 1658 Dihedral : 6.464 56.794 1745 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.27 % Allowed : 18.85 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.25), residues: 1154 helix: 2.15 (0.23), residues: 445 sheet: -0.27 (0.31), residues: 250 loop : 0.03 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP R 264 HIS 0.011 0.001 HIS R 212 PHE 0.018 0.001 PHE R 230 TYR 0.016 0.002 TYR N 115 ARG 0.013 0.001 ARG A 283 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10481.26 seconds wall clock time: 184 minutes 53.90 seconds (11093.90 seconds total)