Starting phenix.real_space_refine on Fri Mar 14 05:54:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rkm_24500/03_2025/7rkm_24500.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rkm_24500/03_2025/7rkm_24500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rkm_24500/03_2025/7rkm_24500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rkm_24500/03_2025/7rkm_24500.map" model { file = "/net/cci-nas-00/data/ceres_data/7rkm_24500/03_2025/7rkm_24500.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rkm_24500/03_2025/7rkm_24500.cif" } resolution = 3.5 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= 0.004 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 6056 2.51 5 N 1604 2.21 5 O 1759 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9491 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1747 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2592 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Conformer: "B" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} bond proxies already assigned to first conformer: 2622 Chain: "C" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "D" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "L" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 531 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 65} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PCA:plan-2': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "R" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2395 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 283} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.31, per 1000 atoms: 0.77 Number of scatterers: 9491 At special positions: 0 Unit cell: (98.4, 134.48, 132.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 1759 8.00 N 1604 7.00 C 6056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.04 Simple disulfide: pdb=" SG CYS L 8 " - pdb=" SG CYS L 34 " distance=2.04 Simple disulfide: pdb=" SG CYS L 12 " - pdb=" SG CYS L 50 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 263 " distance=2.03 Simple disulfide: pdb=" SG CYS R 104 " - pdb=" SG CYS R 173 " 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=0, symmetry=0 Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 1.5 seconds 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 15 sheets defined 36.3% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 8 through 32 removed outlier: 3.701A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.390A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 removed outlier: 3.746A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.784A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.794A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.722A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 10 through 24 Processing helix chain 'C' and resid 29 through 43 Processing helix chain 'C' and resid 44 through 48 removed outlier: 3.625A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.655A pdb=" N SER D 31 " --> pdb=" O ALA D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 56 removed outlier: 3.771A pdb=" N GLY D 56 " --> pdb=" O SER D 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.870A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 6 removed outlier: 3.538A pdb=" N VAL L 5 " --> pdb=" O HIS L 2 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR L 6 " --> pdb=" O HIS L 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 2 through 6' Processing helix chain 'L' and resid 56 through 67 removed outlier: 3.511A pdb=" N ASP L 60 " --> pdb=" O GLN L 56 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP L 66 " --> pdb=" O MET L 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 59 Proline residue: R 34 - end of helix removed outlier: 3.610A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 95 removed outlier: 3.556A pdb=" N VAL R 70 " --> pdb=" O CYS R 66 " (cutoff:3.500A) Proline residue: R 87 - end of helix removed outlier: 4.240A pdb=" N ASP R 95 " --> pdb=" O GLN R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 134 Processing helix chain 'R' and resid 140 through 158 removed outlier: 3.799A pdb=" N LEU R 146 " --> pdb=" O LYS R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 159 through 164 Processing helix chain 'R' and resid 183 through 195 removed outlier: 4.150A pdb=" N GLU R 191 " --> pdb=" O ILE R 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 218 removed outlier: 3.541A pdb=" N VAL R 217 " --> pdb=" O ARG R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 222 through 256 removed outlier: 3.787A pdb=" N VAL R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) Proline residue: R 243 - end of helix Processing helix chain 'R' and resid 263 through 292 removed outlier: 3.527A pdb=" N ARG R 267 " --> pdb=" O CYS R 263 " (cutoff:3.500A) Proline residue: R 288 - end of helix Processing helix chain 'R' and resid 295 through 304 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.082A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.772A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.764A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.206A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.782A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.093A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.670A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.445A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12 removed outlier: 5.972A pdb=" N GLY D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 128 through 130 Processing sheet with id=AB3, first strand: chain 'D' and resid 134 through 136 removed outlier: 4.037A pdb=" N GLU D 234 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU D 162 " --> pdb=" O TYR D 178 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N TYR D 178 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.657A pdb=" N THR L 11 " --> pdb=" O CYS R 23 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 24 through 29 Processing sheet with id=AB6, first strand: chain 'R' and resid 167 through 168 450 hydrogen bonds defined for protein. 1266 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: 2.90 Time building geometry restraints manager: 2.74 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: 2923 1.34 - 1.46: 2284 1.46 - 1.58: 4390 1.58 - 1.71: 0 1.71 - 1.83: 100 Bond restraints: 9697 Sorted by residual: bond pdb=" N PCA L 1 " pdb=" CD PCA L 1 " ideal model delta sigma weight residual 1.345 1.463 -0.118 2.00e-02 2.50e+03 3.46e+01 bond pdb=" CB MET B 262 " pdb=" CG MET B 262 " ideal model delta sigma weight residual 1.520 1.447 0.073 3.00e-02 1.11e+03 5.88e+00 bond pdb=" C ILE R 160 " pdb=" N PRO R 161 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.96e+00 bond pdb=" SD MET B 262 " pdb=" CE MET B 262 " ideal model delta sigma weight residual 1.791 1.736 0.055 2.50e-02 1.60e+03 4.88e+00 bond pdb=" C ASN R 287 " pdb=" N PRO R 288 " ideal model delta sigma weight residual 1.335 1.359 -0.025 1.28e-02 6.10e+03 3.72e+00 ... (remaining 9692 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.60: 13054 4.60 - 9.19: 84 9.19 - 13.79: 5 13.79 - 18.39: 0 18.39 - 22.99: 1 Bond angle restraints: 13144 Sorted by residual: angle pdb=" CB MET B 262 " pdb=" CG MET B 262 " pdb=" SD MET B 262 " ideal model delta sigma weight residual 112.70 89.71 22.99 3.00e+00 1.11e-01 5.87e+01 angle pdb=" C ARG D 179 " pdb=" N MET D 180 " pdb=" CA MET D 180 " ideal model delta sigma weight residual 121.54 131.97 -10.43 1.91e+00 2.74e-01 2.98e+01 angle pdb=" CB MET R 174 " pdb=" CG MET R 174 " pdb=" SD MET R 174 " ideal model delta sigma weight residual 112.70 125.74 -13.04 3.00e+00 1.11e-01 1.89e+01 angle pdb=" N MET D 180 " pdb=" CA MET D 180 " pdb=" CB MET D 180 " ideal model delta sigma weight residual 110.49 117.48 -6.99 1.69e+00 3.50e-01 1.71e+01 angle pdb=" N ASN R 287 " pdb=" CA ASN R 287 " pdb=" C ASN R 287 " ideal model delta sigma weight residual 113.16 118.58 -5.42 1.42e+00 4.96e-01 1.46e+01 ... (remaining 13139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 5410 17.94 - 35.89: 329 35.89 - 53.83: 71 53.83 - 71.77: 7 71.77 - 89.72: 4 Dihedral angle restraints: 5821 sinusoidal: 2317 harmonic: 3504 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 158.42 -65.42 1 1.00e+01 1.00e-02 5.61e+01 dihedral pdb=" CB CYS R 23 " pdb=" SG CYS R 23 " pdb=" SG CYS R 263 " pdb=" CB CYS R 263 " ideal model delta sinusoidal sigma weight residual -86.00 -131.88 45.88 1 1.00e+01 1.00e-02 2.92e+01 dihedral pdb=" CA ILE R 259 " pdb=" C ILE R 259 " pdb=" N SER R 260 " pdb=" CA SER R 260 " ideal model delta harmonic sigma weight residual 180.00 154.33 25.67 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 5818 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1248 0.073 - 0.146: 209 0.146 - 0.219: 23 0.219 - 0.292: 9 0.292 - 0.365: 4 Chirality restraints: 1493 Sorted by residual: chirality pdb=" CA ASN R 287 " pdb=" N ASN R 287 " pdb=" C ASN R 287 " pdb=" CB ASN R 287 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CB THR A 324 " pdb=" CA THR A 324 " pdb=" OG1 THR A 324 " pdb=" CG2 THR A 324 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.62 0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 1490 not shown) Planarity restraints: 1654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 57 " -0.014 2.00e-02 2.50e+03 1.69e-02 7.11e+00 pdb=" CG TRP L 57 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP L 57 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP L 57 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP L 57 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP L 57 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP L 57 " -0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 57 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 57 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP L 57 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 44 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.45e+00 pdb=" C PHE R 44 " 0.044 2.00e-02 2.50e+03 pdb=" O PHE R 44 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU R 45 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 94 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.95e+00 pdb=" C LEU R 94 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU R 94 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP R 95 " 0.014 2.00e-02 2.50e+03 ... (remaining 1651 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 447 2.73 - 3.27: 9397 3.27 - 3.81: 15586 3.81 - 4.36: 19326 4.36 - 4.90: 33285 Nonbonded interactions: 78041 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.181 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.199 3.040 nonbonded pdb=" OD1 ASN R 189 " pdb=" OG1 THR R 252 " model vdw 2.206 3.040 nonbonded pdb=" O LEU R 53 " pdb=" OG1 THR R 57 " model vdw 2.223 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.241 3.040 ... (remaining 78036 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.490 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.500 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 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 : 0.005 0.118 9697 Z= 0.349 Angle : 0.970 22.986 13144 Z= 0.501 Chirality : 0.060 0.365 1493 Planarity : 0.005 0.042 1654 Dihedral : 12.319 89.718 3536 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.13 (0.24), residues: 1183 helix: 0.52 (0.26), residues: 400 sheet: -1.09 (0.29), residues: 288 loop : -1.52 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP L 57 HIS 0.009 0.002 HIS B 54 PHE 0.024 0.003 PHE D 68 TYR 0.024 0.003 TYR A 320 ARG 0.009 0.001 ARG D 148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.182 Fit side-chains REVERT: A 26 ASP cc_start: 0.7340 (m-30) cc_final: 0.6893 (m-30) REVERT: D 6 GLU cc_start: 0.7503 (mp0) cc_final: 0.7194 (mp0) REVERT: D 127 VAL cc_start: 0.8911 (p) cc_final: 0.8640 (t) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2649 time to fit residues: 63.8999 Evaluate side-chains 143 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 189 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.136786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.110389 restraints weight = 16196.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.109712 restraints weight = 15138.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111708 restraints weight = 13070.405| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3390 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9697 Z= 0.221 Angle : 0.601 7.772 13144 Z= 0.318 Chirality : 0.044 0.184 1493 Planarity : 0.003 0.037 1654 Dihedral : 4.998 35.839 1370 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.87 % Allowed : 8.29 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.89 (0.24), residues: 1183 helix: 0.92 (0.27), residues: 403 sheet: -0.95 (0.29), residues: 283 loop : -1.60 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 57 HIS 0.005 0.001 HIS R 245 PHE 0.030 0.002 PHE A 334 TYR 0.029 0.002 TYR R 92 ARG 0.003 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 1.045 Fit side-chains REVERT: A 26 ASP cc_start: 0.7337 (m-30) cc_final: 0.6910 (m-30) REVERT: A 52 GLN cc_start: 0.7072 (tm-30) cc_final: 0.6767 (tt0) REVERT: A 248 LYS cc_start: 0.8196 (mttm) cc_final: 0.7911 (tptp) REVERT: B 247 ASP cc_start: 0.6910 (t70) cc_final: 0.6675 (t0) REVERT: D 6 GLU cc_start: 0.7351 (mp0) cc_final: 0.7097 (mp0) REVERT: R 191 GLU cc_start: 0.7812 (tt0) cc_final: 0.7584 (tt0) outliers start: 9 outliers final: 6 residues processed: 162 average time/residue: 0.2401 time to fit residues: 53.9924 Evaluate side-chains 144 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 138 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 178 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 45 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 74 optimal weight: 0.3980 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN D 3 GLN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 45 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.136673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.110766 restraints weight = 24071.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.114612 restraints weight = 27412.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.115805 restraints weight = 12370.532| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9697 Z= 0.217 Angle : 0.584 7.794 13144 Z= 0.307 Chirality : 0.043 0.237 1493 Planarity : 0.003 0.039 1654 Dihedral : 4.927 37.157 1370 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.93 % Allowed : 9.93 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.73 (0.24), residues: 1183 helix: 1.11 (0.27), residues: 403 sheet: -0.96 (0.29), residues: 286 loop : -1.49 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS R 245 PHE 0.024 0.002 PHE A 334 TYR 0.030 0.002 TYR R 92 ARG 0.004 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 1.039 Fit side-chains REVERT: A 26 ASP cc_start: 0.7356 (m-30) cc_final: 0.6937 (m-30) REVERT: B 247 ASP cc_start: 0.6924 (t70) cc_final: 0.6668 (t0) outliers start: 20 outliers final: 11 residues processed: 159 average time/residue: 0.2236 time to fit residues: 49.4077 Evaluate side-chains 149 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain L residue 8 CYS Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 178 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 86 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 9 ASN L 26 HIS L 45 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.135075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.110567 restraints weight = 24217.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.111443 restraints weight = 26383.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.113100 restraints weight = 17460.802| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3401 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9697 Z= 0.261 Angle : 0.598 7.920 13144 Z= 0.313 Chirality : 0.043 0.218 1493 Planarity : 0.003 0.042 1654 Dihedral : 4.949 36.669 1370 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.93 % Allowed : 11.28 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.69 (0.24), residues: 1183 helix: 1.13 (0.27), residues: 403 sheet: -0.96 (0.29), residues: 286 loop : -1.43 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 99 HIS 0.006 0.001 HIS B 142 PHE 0.021 0.002 PHE A 334 TYR 0.032 0.002 TYR R 92 ARG 0.004 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.957 Fit side-chains REVERT: A 26 ASP cc_start: 0.7384 (m-30) cc_final: 0.6945 (m-30) REVERT: A 52 GLN cc_start: 0.7004 (tm-30) cc_final: 0.6468 (tt0) REVERT: B 247 ASP cc_start: 0.7068 (t70) cc_final: 0.6561 (t0) REVERT: D 180 MET cc_start: 0.7813 (ptm) cc_final: 0.7437 (ptm) REVERT: L 16 THR cc_start: 0.6497 (m) cc_final: 0.6281 (p) REVERT: R 16 TYR cc_start: 0.6512 (p90) cc_final: 0.6294 (p90) outliers start: 20 outliers final: 13 residues processed: 160 average time/residue: 0.2203 time to fit residues: 49.3905 Evaluate side-chains 150 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 178 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 52 optimal weight: 0.2980 chunk 75 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 106 optimal weight: 0.3980 chunk 109 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 110 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN R 162 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.138237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.111777 restraints weight = 16223.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.110929 restraints weight = 15302.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.113058 restraints weight = 13096.409| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9697 Z= 0.181 Angle : 0.564 8.413 13144 Z= 0.293 Chirality : 0.042 0.191 1493 Planarity : 0.003 0.038 1654 Dihedral : 4.793 36.016 1370 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.25 % Allowed : 13.11 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.55 (0.24), residues: 1183 helix: 1.23 (0.27), residues: 403 sheet: -0.78 (0.29), residues: 280 loop : -1.42 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.006 0.001 HIS R 245 PHE 0.017 0.001 PHE A 334 TYR 0.032 0.001 TYR R 92 ARG 0.006 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 0.979 Fit side-chains REVERT: A 26 ASP cc_start: 0.7292 (m-30) cc_final: 0.6875 (m-30) REVERT: D 180 MET cc_start: 0.7684 (ptm) cc_final: 0.7461 (ptm) REVERT: R 16 TYR cc_start: 0.6539 (p90) cc_final: 0.6336 (p90) outliers start: 13 outliers final: 11 residues processed: 162 average time/residue: 0.2186 time to fit residues: 48.8174 Evaluate side-chains 148 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 178 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 103 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 30 optimal weight: 0.2980 chunk 70 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 45 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.137245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.111298 restraints weight = 16168.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.110140 restraints weight = 13910.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.112385 restraints weight = 12809.503| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3418 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3418 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9697 Z= 0.206 Angle : 0.574 7.705 13144 Z= 0.299 Chirality : 0.043 0.331 1493 Planarity : 0.003 0.038 1654 Dihedral : 4.763 35.779 1370 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.64 % Allowed : 13.40 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.51 (0.25), residues: 1183 helix: 1.27 (0.27), residues: 402 sheet: -0.77 (0.30), residues: 280 loop : -1.39 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.006 0.001 HIS R 245 PHE 0.017 0.001 PHE R 163 TYR 0.033 0.001 TYR R 92 ARG 0.006 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.984 Fit side-chains REVERT: A 26 ASP cc_start: 0.7304 (m-30) cc_final: 0.6862 (m-30) REVERT: C 25 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8338 (mt) REVERT: D 180 MET cc_start: 0.7783 (ptm) cc_final: 0.7510 (ptm) REVERT: R 16 TYR cc_start: 0.6532 (p90) cc_final: 0.6297 (p90) outliers start: 17 outliers final: 12 residues processed: 160 average time/residue: 0.2129 time to fit residues: 48.1725 Evaluate side-chains 152 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 178 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 27 optimal weight: 1.9990 chunk 28 optimal weight: 0.0770 chunk 90 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 74 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN L 45 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.136158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111554 restraints weight = 24268.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.113450 restraints weight = 26455.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.114641 restraints weight = 16873.384| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3423 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9697 Z= 0.227 Angle : 0.582 7.897 13144 Z= 0.304 Chirality : 0.043 0.285 1493 Planarity : 0.003 0.043 1654 Dihedral : 4.768 35.702 1370 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.54 % Allowed : 13.89 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.51 (0.25), residues: 1183 helix: 1.26 (0.27), residues: 402 sheet: -0.79 (0.30), residues: 282 loop : -1.36 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.006 0.001 HIS R 245 PHE 0.016 0.002 PHE R 163 TYR 0.035 0.002 TYR R 92 ARG 0.008 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7384 (m-30) cc_final: 0.6921 (m-30) REVERT: A 52 GLN cc_start: 0.6814 (tm-30) cc_final: 0.6278 (tt0) REVERT: C 25 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8366 (mt) REVERT: D 180 MET cc_start: 0.7756 (ptm) cc_final: 0.7481 (ptm) REVERT: R 16 TYR cc_start: 0.6620 (p90) cc_final: 0.6354 (p90) outliers start: 16 outliers final: 14 residues processed: 161 average time/residue: 0.2135 time to fit residues: 48.1634 Evaluate side-chains 158 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 178 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 107 optimal weight: 0.5980 chunk 55 optimal weight: 0.0870 chunk 76 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 71 optimal weight: 0.0870 chunk 79 optimal weight: 5.9990 chunk 84 optimal weight: 0.5980 chunk 58 optimal weight: 0.4980 chunk 72 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.138753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.111031 restraints weight = 13923.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.112578 restraints weight = 11886.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.113328 restraints weight = 8491.099| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3433 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9697 Z= 0.173 Angle : 0.564 7.683 13144 Z= 0.297 Chirality : 0.042 0.265 1493 Planarity : 0.003 0.044 1654 Dihedral : 4.663 34.790 1370 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.74 % Allowed : 14.27 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.41 (0.25), residues: 1183 helix: 1.34 (0.27), residues: 402 sheet: -0.71 (0.30), residues: 282 loop : -1.32 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS R 245 PHE 0.019 0.001 PHE R 44 TYR 0.034 0.001 TYR R 92 ARG 0.005 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 1.132 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7262 (m-30) cc_final: 0.6836 (m-30) REVERT: A 52 GLN cc_start: 0.6851 (tm-30) cc_final: 0.6287 (tt0) REVERT: C 25 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8351 (mt) REVERT: R 16 TYR cc_start: 0.6613 (p90) cc_final: 0.6354 (p90) REVERT: R 65 GLN cc_start: 0.7617 (mm-40) cc_final: 0.7401 (mm110) REVERT: R 254 LYS cc_start: 0.7468 (tmtt) cc_final: 0.7221 (tttt) outliers start: 18 outliers final: 13 residues processed: 164 average time/residue: 0.2587 time to fit residues: 58.7584 Evaluate side-chains 154 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 178 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 88 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 110 ASN D 3 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.137011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.110909 restraints weight = 16700.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.110086 restraints weight = 12417.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.112082 restraints weight = 11561.520| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3409 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3409 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9697 Z= 0.232 Angle : 0.602 9.862 13144 Z= 0.313 Chirality : 0.043 0.253 1493 Planarity : 0.003 0.043 1654 Dihedral : 4.703 35.148 1370 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.64 % Allowed : 14.66 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.40 (0.25), residues: 1183 helix: 1.33 (0.27), residues: 402 sheet: -0.71 (0.30), residues: 280 loop : -1.30 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.006 0.001 HIS R 245 PHE 0.021 0.002 PHE D 68 TYR 0.034 0.002 TYR R 92 ARG 0.007 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7314 (m-30) cc_final: 0.6851 (m-30) REVERT: C 25 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8376 (mt) REVERT: D 180 MET cc_start: 0.7738 (ptm) cc_final: 0.7524 (ptm) REVERT: R 16 TYR cc_start: 0.6633 (p90) cc_final: 0.6349 (p90) REVERT: R 168 LYS cc_start: 0.6259 (tptm) cc_final: 0.6016 (mmmt) REVERT: R 254 LYS cc_start: 0.7532 (tmtt) cc_final: 0.7173 (tttt) outliers start: 17 outliers final: 15 residues processed: 159 average time/residue: 0.2201 time to fit residues: 48.4519 Evaluate side-chains 160 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 178 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 41 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN D 3 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.137677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.112539 restraints weight = 18791.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.111571 restraints weight = 16168.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.113279 restraints weight = 13079.661| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3415 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3415 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9697 Z= 0.225 Angle : 0.602 9.843 13144 Z= 0.315 Chirality : 0.043 0.253 1493 Planarity : 0.003 0.044 1654 Dihedral : 4.722 35.152 1370 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.54 % Allowed : 15.33 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.40 (0.25), residues: 1183 helix: 1.31 (0.27), residues: 403 sheet: -0.74 (0.30), residues: 281 loop : -1.25 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.006 0.001 HIS R 245 PHE 0.020 0.001 PHE D 68 TYR 0.033 0.002 TYR R 92 ARG 0.007 0.000 ARG D 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7330 (m-30) cc_final: 0.6940 (m-30) REVERT: C 25 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8367 (mt) REVERT: D 180 MET cc_start: 0.7715 (ptm) cc_final: 0.7484 (ptm) REVERT: R 16 TYR cc_start: 0.6691 (p90) cc_final: 0.6411 (p90) outliers start: 16 outliers final: 15 residues processed: 159 average time/residue: 0.2299 time to fit residues: 50.3163 Evaluate side-chains 160 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 178 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 48 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN D 3 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.137293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.111061 restraints weight = 22475.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.114825 restraints weight = 26591.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.115962 restraints weight = 12655.749| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9697 Z= 0.238 Angle : 0.607 9.782 13144 Z= 0.316 Chirality : 0.043 0.245 1493 Planarity : 0.003 0.044 1654 Dihedral : 4.753 35.280 1370 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.45 % Allowed : 15.53 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.39 (0.25), residues: 1183 helix: 1.30 (0.27), residues: 403 sheet: -0.74 (0.30), residues: 280 loop : -1.22 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.006 0.001 HIS R 245 PHE 0.021 0.002 PHE D 68 TYR 0.033 0.002 TYR R 92 ARG 0.007 0.000 ARG D 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3648.86 seconds wall clock time: 65 minutes 37.96 seconds (3937.96 seconds total)