Starting phenix.real_space_refine on Wed Jan 15 03:53:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yrg_39542/01_2025/8yrg_39542.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yrg_39542/01_2025/8yrg_39542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yrg_39542/01_2025/8yrg_39542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yrg_39542/01_2025/8yrg_39542.map" model { file = "/net/cci-nas-00/data/ceres_data/8yrg_39542/01_2025/8yrg_39542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yrg_39542/01_2025/8yrg_39542.cif" } resolution = 3.14 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= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 51 5.16 5 C 5097 2.51 5 N 1368 2.21 5 O 1460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 7977 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1675 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 6, 'TRANS': 215} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 94 Chain: "C" Number of atoms: 2477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2477 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 92 Chain: "D" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 353 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1730 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1723 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 8, 'TRANS': 228} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 79 Chain: "R" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'A1LZU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.51, per 1000 atoms: 0.69 Number of scatterers: 7977 At special positions: 0 Unit cell: (88, 115.28, 125.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 51 16.00 P 1 15.00 O 1460 8.00 N 1368 7.00 C 5097 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 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: 2.29 Conformation dependent library (CDL) restraints added in 981.5 milliseconds 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2018 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 36.4% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'B' and resid 6 through 31 Processing helix chain 'B' and resid 95 through 102 removed outlier: 4.043A pdb=" N GLN B 98 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASP B 102 " --> pdb=" O CYS B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 131 through 135 removed outlier: 3.788A pdb=" N ARG B 135 " --> pdb=" O ARG B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.542A pdb=" N LEU B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY B 156 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 164 removed outlier: 3.954A pdb=" N TYR B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 168 removed outlier: 4.334A pdb=" N ALA B 168 " --> pdb=" O PRO B 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 165 through 168' Processing helix chain 'B' and resid 183 through 202 removed outlier: 3.714A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 243 removed outlier: 4.035A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 25 Processing helix chain 'C' and resid 29 through 35 Processing helix chain 'D' and resid 12 through 24 removed outlier: 4.199A pdb=" N VAL D 16 " --> pdb=" O ALA D 12 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 43 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.878A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.000A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 55 Processing helix chain 'R' and resid 61 through 86 Proline residue: R 84 - end of helix Processing helix chain 'R' and resid 91 through 126 Proline residue: R 105 - end of helix removed outlier: 4.003A pdb=" N THR R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER R 117 " --> pdb=" O LEU R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 133 Processing helix chain 'R' and resid 137 through 153 removed outlier: 3.943A pdb=" N LEU R 151 " --> pdb=" O TRP R 147 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU R 152 " --> pdb=" O GLY R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 204 removed outlier: 3.771A pdb=" N ILE R 202 " --> pdb=" O LEU R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 228 removed outlier: 3.928A pdb=" N TYR R 215 " --> pdb=" O LEU R 211 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL R 216 " --> pdb=" O THR R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 242 removed outlier: 4.664A pdb=" N GLY R 233 " --> pdb=" O GLY R 229 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA R 237 " --> pdb=" O GLY R 233 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N TYR R 240 " --> pdb=" O GLY R 236 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG R 241 " --> pdb=" O ALA R 237 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 274 removed outlier: 4.145A pdb=" N CYS R 251 " --> pdb=" O GLU R 247 " (cutoff:3.500A) Proline residue: R 269 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 76 removed outlier: 4.644A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.551A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER C 331 " --> pdb=" O PHE C 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.692A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.885A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 153 removed outlier: 3.740A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.634A pdb=" N SER C 189 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.508A pdb=" N ALA C 231 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.345A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS C 294 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 5.025A pdb=" N CYS E 96 " --> pdb=" O GLY E 112 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY E 114 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N TYR E 94 " --> pdb=" O GLY E 114 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR E 116 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA E 92 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 134 through 135 Processing sheet with id=AB3, first strand: chain 'E' and resid 144 through 147 Processing sheet with id=AB4, first strand: chain 'E' and resid 182 through 183 removed outlier: 6.540A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) 401 hydrogen bonds defined for protein. 1149 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: 2.47 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2579 1.34 - 1.46: 1961 1.46 - 1.58: 3528 1.58 - 1.70: 1 1.70 - 1.82: 71 Bond restraints: 8140 Sorted by residual: bond pdb=" O2 A1LZU R 501 " pdb=" P1 A1LZU R 501 " ideal model delta sigma weight residual 1.740 1.617 0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" C13 A1LZU R 501 " pdb=" O2 A1LZU R 501 " ideal model delta sigma weight residual 1.364 1.403 -0.039 2.00e-02 2.50e+03 3.74e+00 bond pdb=" CB CYS C 103 " pdb=" SG CYS C 103 " ideal model delta sigma weight residual 1.808 1.756 0.052 3.30e-02 9.18e+02 2.48e+00 bond pdb=" CG PRO E 224 " pdb=" CD PRO E 224 " ideal model delta sigma weight residual 1.512 1.472 0.040 2.70e-02 1.37e+03 2.20e+00 bond pdb=" CG1 ILE C 273 " pdb=" CD1 ILE C 273 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.14e+00 ... (remaining 8135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 10860 1.92 - 3.85: 196 3.85 - 5.77: 22 5.77 - 7.69: 9 7.69 - 9.62: 4 Bond angle restraints: 11091 Sorted by residual: angle pdb=" N GLU B 25 " pdb=" CA GLU B 25 " pdb=" CB GLU B 25 " ideal model delta sigma weight residual 110.16 114.75 -4.59 1.48e+00 4.57e-01 9.61e+00 angle pdb=" C GLN E 113 " pdb=" N GLY E 114 " pdb=" CA GLY E 114 " ideal model delta sigma weight residual 121.58 119.14 2.44 8.60e-01 1.35e+00 8.05e+00 angle pdb=" N VAL R 101 " pdb=" CA VAL R 101 " pdb=" C VAL R 101 " ideal model delta sigma weight residual 113.00 109.41 3.59 1.30e+00 5.92e-01 7.64e+00 angle pdb=" CA LEU C 70 " pdb=" CB LEU C 70 " pdb=" CG LEU C 70 " ideal model delta sigma weight residual 116.30 125.92 -9.62 3.50e+00 8.16e-02 7.55e+00 angle pdb=" O1 A1LZU R 501 " pdb=" C13 A1LZU R 501 " pdb=" O2 A1LZU R 501 " ideal model delta sigma weight residual 106.35 113.87 -7.52 3.00e+00 1.11e-01 6.29e+00 ... (remaining 11086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 4343 16.52 - 33.04: 340 33.04 - 49.56: 71 49.56 - 66.07: 6 66.07 - 82.59: 5 Dihedral angle restraints: 4765 sinusoidal: 1640 harmonic: 3125 Sorted by residual: dihedral pdb=" CA LEU R 156 " pdb=" C LEU R 156 " pdb=" N GLU R 157 " pdb=" CA GLU R 157 " ideal model delta harmonic sigma weight residual -180.00 -160.66 -19.34 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA LEU B 34 " pdb=" C LEU B 34 " pdb=" N ARG B 35 " pdb=" CA ARG B 35 " ideal model delta harmonic sigma weight residual -180.00 -160.78 -19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA PHE C 234 " pdb=" C PHE C 234 " pdb=" N PHE C 235 " pdb=" CA PHE C 235 " ideal model delta harmonic sigma weight residual 180.00 161.40 18.60 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 4762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 949 0.049 - 0.097: 297 0.097 - 0.146: 56 0.146 - 0.194: 2 0.194 - 0.243: 1 Chirality restraints: 1305 Sorted by residual: chirality pdb=" CG LEU B 245 " pdb=" CB LEU B 245 " pdb=" CD1 LEU B 245 " pdb=" CD2 LEU B 245 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB ILE R 179 " pdb=" CA ILE R 179 " pdb=" CG1 ILE R 179 " pdb=" CG2 ILE R 179 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.23e-01 chirality pdb=" CG LEU E 79 " pdb=" CB LEU E 79 " pdb=" CD1 LEU E 79 " pdb=" CD2 LEU E 79 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.79e-01 ... (remaining 1302 not shown) Planarity restraints: 1399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 212 " -0.034 5.00e-02 4.00e+02 5.12e-02 4.19e+00 pdb=" N PRO B 213 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 213 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 213 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 48 " -0.031 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO D 49 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 49 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 49 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS R 251 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.08e+00 pdb=" C CYS R 251 " -0.030 2.00e-02 2.50e+03 pdb=" O CYS R 251 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS R 252 " 0.010 2.00e-02 2.50e+03 ... (remaining 1396 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 92 2.65 - 3.22: 7321 3.22 - 3.78: 11892 3.78 - 4.34: 16092 4.34 - 4.90: 27578 Nonbonded interactions: 62975 Sorted by model distance: nonbonded pdb=" OH TYR R 106 " pdb=" O GLY R 229 " model vdw 2.093 3.040 nonbonded pdb=" OG SER C 74 " pdb=" OD1 ASP C 76 " model vdw 2.101 3.040 nonbonded pdb=" O ILE E 100 " pdb=" OG SER E 105 " model vdw 2.147 3.040 nonbonded pdb=" OE2 GLU B 8 " pdb=" OH TYR E 163 " model vdw 2.192 3.040 nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.212 3.040 ... (remaining 62970 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: 1.030 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: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.630 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 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 : 0.007 0.123 8140 Z= 0.456 Angle : 0.691 9.616 11091 Z= 0.370 Chirality : 0.046 0.243 1305 Planarity : 0.004 0.051 1399 Dihedral : 12.794 82.592 2741 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: -0.87 (0.25), residues: 1061 helix: 0.68 (0.27), residues: 350 sheet: -0.72 (0.30), residues: 286 loop : -1.46 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 339 HIS 0.009 0.002 HIS C 225 PHE 0.024 0.002 PHE C 151 TYR 0.023 0.002 TYR R 106 ARG 0.011 0.001 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.990 Fit side-chains REVERT: B 9 ASP cc_start: 0.6826 (m-30) cc_final: 0.6526 (m-30) REVERT: B 95 LYS cc_start: 0.7406 (tppp) cc_final: 0.6586 (tppp) REVERT: C 118 ASP cc_start: 0.6887 (p0) cc_final: 0.6539 (p0) REVERT: C 155 ASN cc_start: 0.7411 (p0) cc_final: 0.7207 (p0) REVERT: C 204 CYS cc_start: 0.7084 (m) cc_final: 0.6754 (m) REVERT: C 277 SER cc_start: 0.8098 (t) cc_final: 0.7768 (p) REVERT: C 298 ASP cc_start: 0.7208 (t70) cc_final: 0.6938 (t70) REVERT: C 333 ASP cc_start: 0.7068 (p0) cc_final: 0.6761 (p0) REVERT: R 112 MET cc_start: 0.7789 (mmt) cc_final: 0.7220 (mmt) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.2355 time to fit residues: 61.6425 Evaluate side-chains 187 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 0.0570 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.142940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.122943 restraints weight = 11838.592| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.37 r_work: 0.3404 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8140 Z= 0.239 Angle : 0.594 9.720 11091 Z= 0.306 Chirality : 0.043 0.177 1305 Planarity : 0.004 0.050 1399 Dihedral : 4.657 24.221 1173 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.89 % Allowed : 10.70 % Favored : 88.41 % 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: -0.28 (0.26), residues: 1061 helix: 1.26 (0.28), residues: 352 sheet: -0.21 (0.30), residues: 290 loop : -1.39 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 63 HIS 0.004 0.001 HIS C 225 PHE 0.015 0.002 PHE R 273 TYR 0.020 0.002 TYR R 106 ARG 0.005 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 214 time to evaluate : 0.876 Fit side-chains REVERT: B 9 ASP cc_start: 0.7128 (m-30) cc_final: 0.6790 (m-30) REVERT: B 17 LYS cc_start: 0.7869 (mtmm) cc_final: 0.7667 (mtmm) REVERT: B 95 LYS cc_start: 0.7771 (tppp) cc_final: 0.7184 (tppp) REVERT: B 130 ASN cc_start: 0.8485 (m-40) cc_final: 0.8270 (m-40) REVERT: C 118 ASP cc_start: 0.7092 (p0) cc_final: 0.6711 (p0) REVERT: C 135 VAL cc_start: 0.8177 (t) cc_final: 0.7905 (m) REVERT: C 155 ASN cc_start: 0.7651 (p0) cc_final: 0.7351 (p0) REVERT: C 204 CYS cc_start: 0.7635 (m) cc_final: 0.7419 (m) REVERT: C 251 ARG cc_start: 0.8102 (mtt-85) cc_final: 0.7767 (mtt-85) REVERT: C 277 SER cc_start: 0.8314 (t) cc_final: 0.7975 (p) REVERT: C 298 ASP cc_start: 0.7812 (t70) cc_final: 0.7437 (t70) REVERT: C 333 ASP cc_start: 0.7293 (p0) cc_final: 0.7091 (p0) REVERT: E 34 MET cc_start: 0.7991 (mmt) cc_final: 0.7755 (mmm) REVERT: E 218 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7591 (ttp) REVERT: R 223 LEU cc_start: 0.8237 (mp) cc_final: 0.7834 (mp) outliers start: 7 outliers final: 5 residues processed: 214 average time/residue: 0.2332 time to fit residues: 65.0949 Evaluate side-chains 218 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 212 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain R residue 114 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 62 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 32 optimal weight: 0.0050 chunk 54 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.143518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.124294 restraints weight = 12019.171| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.33 r_work: 0.3417 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8140 Z= 0.196 Angle : 0.559 10.092 11091 Z= 0.284 Chirality : 0.042 0.196 1305 Planarity : 0.004 0.045 1399 Dihedral : 4.301 23.721 1173 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.29 % Allowed : 12.99 % Favored : 84.71 % 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: 0.06 (0.26), residues: 1061 helix: 1.68 (0.29), residues: 352 sheet: 0.03 (0.30), residues: 293 loop : -1.38 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.021 0.001 PHE R 273 TYR 0.015 0.001 TYR R 106 ARG 0.003 0.000 ARG C 283 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 0.870 Fit side-chains REVERT: B 25 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6303 (mp0) REVERT: B 95 LYS cc_start: 0.7762 (tppp) cc_final: 0.7182 (tppp) REVERT: C 118 ASP cc_start: 0.6958 (p0) cc_final: 0.6543 (p0) REVERT: C 135 VAL cc_start: 0.8131 (t) cc_final: 0.7884 (m) REVERT: C 155 ASN cc_start: 0.7654 (p0) cc_final: 0.7373 (p0) REVERT: C 298 ASP cc_start: 0.7748 (t70) cc_final: 0.7409 (t70) REVERT: E 34 MET cc_start: 0.7948 (mmt) cc_final: 0.7714 (mmm) REVERT: E 218 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7565 (ttp) REVERT: R 223 LEU cc_start: 0.8200 (mp) cc_final: 0.7790 (mp) outliers start: 18 outliers final: 14 residues processed: 215 average time/residue: 0.2320 time to fit residues: 65.0823 Evaluate side-chains 221 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 155 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 91 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.142606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.123528 restraints weight = 11934.010| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.32 r_work: 0.3408 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8140 Z= 0.263 Angle : 0.582 10.069 11091 Z= 0.295 Chirality : 0.042 0.213 1305 Planarity : 0.004 0.045 1399 Dihedral : 4.343 22.149 1173 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.06 % Allowed : 15.29 % Favored : 81.66 % 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: 0.08 (0.26), residues: 1061 helix: 1.68 (0.28), residues: 352 sheet: 0.03 (0.30), residues: 294 loop : -1.36 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 169 HIS 0.004 0.001 HIS B 214 PHE 0.023 0.002 PHE R 273 TYR 0.018 0.002 TYR E 178 ARG 0.006 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: B 9 ASP cc_start: 0.7151 (m-30) cc_final: 0.6802 (m-30) REVERT: C 135 VAL cc_start: 0.8138 (t) cc_final: 0.7901 (m) REVERT: C 137 ARG cc_start: 0.7275 (ttm-80) cc_final: 0.6997 (ttm-80) REVERT: C 155 ASN cc_start: 0.7634 (p0) cc_final: 0.7339 (p0) REVERT: C 298 ASP cc_start: 0.7762 (t70) cc_final: 0.7412 (t70) REVERT: R 112 MET cc_start: 0.8143 (mmt) cc_final: 0.7499 (mmt) REVERT: R 223 LEU cc_start: 0.8207 (mp) cc_final: 0.7793 (mp) outliers start: 24 outliers final: 16 residues processed: 216 average time/residue: 0.2223 time to fit residues: 63.4043 Evaluate side-chains 228 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 212 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 264 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 2 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 80 optimal weight: 0.0370 chunk 9 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.142989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.123901 restraints weight = 11838.127| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.33 r_work: 0.3412 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8140 Z= 0.224 Angle : 0.568 10.320 11091 Z= 0.287 Chirality : 0.042 0.226 1305 Planarity : 0.004 0.043 1399 Dihedral : 4.216 22.415 1173 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.06 % Allowed : 15.80 % Favored : 81.15 % 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: 0.23 (0.26), residues: 1061 helix: 1.82 (0.28), residues: 353 sheet: 0.07 (0.30), residues: 294 loop : -1.25 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 63 HIS 0.004 0.001 HIS E 35 PHE 0.027 0.001 PHE R 273 TYR 0.016 0.001 TYR E 178 ARG 0.004 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 212 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: B 9 ASP cc_start: 0.7139 (m-30) cc_final: 0.6794 (m-30) REVERT: B 17 LYS cc_start: 0.7831 (mtmm) cc_final: 0.7589 (mtmm) REVERT: C 118 ASP cc_start: 0.6966 (p0) cc_final: 0.6565 (p0) REVERT: C 135 VAL cc_start: 0.8118 (t) cc_final: 0.7912 (m) REVERT: C 155 ASN cc_start: 0.7621 (p0) cc_final: 0.7346 (p0) REVERT: C 200 VAL cc_start: 0.8686 (m) cc_final: 0.8348 (p) REVERT: C 298 ASP cc_start: 0.7756 (t70) cc_final: 0.7413 (t70) REVERT: C 333 ASP cc_start: 0.7108 (p0) cc_final: 0.6898 (p0) REVERT: E 34 MET cc_start: 0.7931 (mmt) cc_final: 0.7642 (mmm) REVERT: E 83 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.6916 (mmt) REVERT: R 112 MET cc_start: 0.8173 (mmt) cc_final: 0.7554 (mmt) REVERT: R 122 LEU cc_start: 0.8649 (mm) cc_final: 0.8379 (mt) REVERT: R 129 TRP cc_start: 0.8278 (t60) cc_final: 0.7787 (t60) REVERT: R 223 LEU cc_start: 0.8207 (mp) cc_final: 0.7793 (mp) outliers start: 24 outliers final: 19 residues processed: 220 average time/residue: 0.2146 time to fit residues: 62.7289 Evaluate side-chains 224 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 264 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 chunk 103 optimal weight: 0.6980 chunk 41 optimal weight: 0.0870 chunk 72 optimal weight: 0.0770 chunk 1 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.144001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.124910 restraints weight = 11929.285| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.32 r_work: 0.3424 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8140 Z= 0.197 Angle : 0.567 10.207 11091 Z= 0.284 Chirality : 0.041 0.239 1305 Planarity : 0.003 0.040 1399 Dihedral : 4.103 23.171 1173 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.82 % Allowed : 15.29 % Favored : 80.89 % 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: 0.35 (0.27), residues: 1061 helix: 1.96 (0.29), residues: 353 sheet: 0.14 (0.30), residues: 294 loop : -1.23 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 63 HIS 0.003 0.001 HIS E 35 PHE 0.027 0.001 PHE R 273 TYR 0.015 0.001 TYR E 178 ARG 0.004 0.000 ARG C 283 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.7869 (mtmm) cc_final: 0.7602 (mtmm) REVERT: B 111 ASP cc_start: 0.7391 (t0) cc_final: 0.7150 (t0) REVERT: C 118 ASP cc_start: 0.6950 (p0) cc_final: 0.6566 (p0) REVERT: C 155 ASN cc_start: 0.7663 (p0) cc_final: 0.7386 (p0) REVERT: C 200 VAL cc_start: 0.8701 (m) cc_final: 0.8339 (p) REVERT: C 228 ASP cc_start: 0.6834 (OUTLIER) cc_final: 0.6361 (m-30) REVERT: C 298 ASP cc_start: 0.7693 (t70) cc_final: 0.7370 (t70) REVERT: E 83 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.6910 (mmt) REVERT: E 128 MET cc_start: 0.8104 (ptt) cc_final: 0.7813 (ptm) REVERT: R 112 MET cc_start: 0.8177 (mmt) cc_final: 0.7455 (mmt) REVERT: R 129 TRP cc_start: 0.8262 (t60) cc_final: 0.7753 (t60) outliers start: 30 outliers final: 21 residues processed: 215 average time/residue: 0.2178 time to fit residues: 61.6846 Evaluate side-chains 224 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 264 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 39 optimal weight: 0.0670 chunk 27 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 35 optimal weight: 0.7980 chunk 88 optimal weight: 0.0670 chunk 22 optimal weight: 20.0000 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.144413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.125176 restraints weight = 11991.912| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.35 r_work: 0.3432 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8140 Z= 0.168 Angle : 0.548 9.708 11091 Z= 0.275 Chirality : 0.041 0.250 1305 Planarity : 0.003 0.038 1399 Dihedral : 3.959 23.311 1173 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.06 % Allowed : 16.69 % Favored : 80.25 % 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: 0.50 (0.27), residues: 1061 helix: 2.15 (0.29), residues: 353 sheet: 0.18 (0.30), residues: 294 loop : -1.17 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.028 0.001 PHE R 273 TYR 0.013 0.001 TYR E 178 ARG 0.005 0.000 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.7847 (mtmm) cc_final: 0.7583 (mtmm) REVERT: B 111 ASP cc_start: 0.7404 (t0) cc_final: 0.7149 (t0) REVERT: C 155 ASN cc_start: 0.7641 (p0) cc_final: 0.7368 (p0) REVERT: C 200 VAL cc_start: 0.8689 (m) cc_final: 0.8279 (p) REVERT: C 228 ASP cc_start: 0.6834 (OUTLIER) cc_final: 0.6379 (m-30) REVERT: C 234 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.7847 (m-80) REVERT: C 280 LYS cc_start: 0.8020 (tttp) cc_final: 0.7793 (tttp) REVERT: C 298 ASP cc_start: 0.7651 (t70) cc_final: 0.7392 (t70) REVERT: R 74 LEU cc_start: 0.7708 (tp) cc_final: 0.7290 (mp) REVERT: R 112 MET cc_start: 0.8152 (mmt) cc_final: 0.7462 (mmt) REVERT: R 122 LEU cc_start: 0.8587 (mm) cc_final: 0.8263 (mt) REVERT: R 129 TRP cc_start: 0.8250 (t60) cc_final: 0.7679 (t60) REVERT: R 223 LEU cc_start: 0.8217 (mp) cc_final: 0.7823 (mp) outliers start: 24 outliers final: 18 residues processed: 216 average time/residue: 0.2312 time to fit residues: 65.5340 Evaluate side-chains 227 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 207 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 264 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 102 optimal weight: 0.5980 chunk 39 optimal weight: 0.1980 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 chunk 17 optimal weight: 0.3980 chunk 66 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.144328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.125039 restraints weight = 11979.372| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.34 r_work: 0.3432 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8140 Z= 0.193 Angle : 0.571 10.237 11091 Z= 0.284 Chirality : 0.041 0.254 1305 Planarity : 0.003 0.038 1399 Dihedral : 3.986 24.061 1173 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.31 % Allowed : 17.45 % Favored : 79.24 % 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: 0.52 (0.27), residues: 1061 helix: 2.13 (0.29), residues: 353 sheet: 0.17 (0.30), residues: 296 loop : -1.11 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 169 HIS 0.004 0.001 HIS E 35 PHE 0.024 0.001 PHE R 273 TYR 0.016 0.001 TYR E 178 ARG 0.005 0.000 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.7874 (mtmm) cc_final: 0.7623 (mtmm) REVERT: B 111 ASP cc_start: 0.7388 (t0) cc_final: 0.7126 (t0) REVERT: C 155 ASN cc_start: 0.7626 (p0) cc_final: 0.7358 (p0) REVERT: C 200 VAL cc_start: 0.8681 (m) cc_final: 0.8257 (p) REVERT: C 228 ASP cc_start: 0.6818 (OUTLIER) cc_final: 0.6369 (m-30) REVERT: C 234 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.7850 (m-80) REVERT: C 280 LYS cc_start: 0.8025 (tttp) cc_final: 0.7797 (tttp) REVERT: C 298 ASP cc_start: 0.7661 (t70) cc_final: 0.7400 (t70) REVERT: E 83 MET cc_start: 0.7828 (mtm) cc_final: 0.7463 (mtt) REVERT: R 112 MET cc_start: 0.8130 (mmt) cc_final: 0.7404 (mmt) REVERT: R 122 LEU cc_start: 0.8581 (mm) cc_final: 0.8257 (mt) REVERT: R 129 TRP cc_start: 0.8256 (t60) cc_final: 0.7734 (t60) REVERT: R 223 LEU cc_start: 0.8195 (mp) cc_final: 0.7814 (mp) outliers start: 26 outliers final: 23 residues processed: 215 average time/residue: 0.2201 time to fit residues: 62.5667 Evaluate side-chains 229 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 264 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 0 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 0.1980 chunk 69 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 75 optimal weight: 0.2980 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.144624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.125295 restraints weight = 12039.295| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.35 r_work: 0.3434 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8140 Z= 0.189 Angle : 0.570 10.400 11091 Z= 0.284 Chirality : 0.041 0.256 1305 Planarity : 0.003 0.038 1399 Dihedral : 3.942 23.729 1173 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.31 % Allowed : 17.96 % Favored : 78.73 % 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: 0.58 (0.27), residues: 1061 helix: 2.19 (0.29), residues: 353 sheet: 0.19 (0.30), residues: 296 loop : -1.08 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.023 0.001 PHE R 273 TYR 0.015 0.001 TYR E 178 ARG 0.005 0.000 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 204 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.7862 (mtmm) cc_final: 0.7613 (mtmm) REVERT: B 111 ASP cc_start: 0.7407 (t0) cc_final: 0.7143 (t0) REVERT: C 155 ASN cc_start: 0.7634 (p0) cc_final: 0.7380 (p0) REVERT: C 200 VAL cc_start: 0.8675 (m) cc_final: 0.8258 (p) REVERT: C 228 ASP cc_start: 0.6831 (OUTLIER) cc_final: 0.6367 (m-30) REVERT: C 234 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.7843 (m-80) REVERT: C 280 LYS cc_start: 0.8027 (tttp) cc_final: 0.7806 (tttp) REVERT: C 298 ASP cc_start: 0.7637 (t70) cc_final: 0.7397 (t70) REVERT: E 128 MET cc_start: 0.8018 (ptt) cc_final: 0.7618 (ptm) REVERT: R 112 MET cc_start: 0.8140 (mmt) cc_final: 0.7416 (mmt) REVERT: R 122 LEU cc_start: 0.8582 (mm) cc_final: 0.8257 (mt) REVERT: R 129 TRP cc_start: 0.8258 (t60) cc_final: 0.7737 (t60) REVERT: R 213 ARG cc_start: 0.7332 (ttt180) cc_final: 0.7031 (ttt180) REVERT: R 223 LEU cc_start: 0.8198 (mp) cc_final: 0.7812 (mp) outliers start: 26 outliers final: 21 residues processed: 214 average time/residue: 0.2229 time to fit residues: 62.8507 Evaluate side-chains 226 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 264 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 76 optimal weight: 0.0770 chunk 20 optimal weight: 0.3980 chunk 57 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.144449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.125209 restraints weight = 11920.724| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.33 r_work: 0.3436 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8140 Z= 0.204 Angle : 0.579 10.727 11091 Z= 0.289 Chirality : 0.042 0.257 1305 Planarity : 0.003 0.039 1399 Dihedral : 3.981 23.240 1173 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.06 % Allowed : 18.47 % Favored : 78.47 % 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: 0.57 (0.27), residues: 1061 helix: 2.19 (0.29), residues: 353 sheet: 0.13 (0.30), residues: 298 loop : -1.04 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 169 HIS 0.004 0.001 HIS E 35 PHE 0.029 0.001 PHE R 273 TYR 0.016 0.001 TYR E 178 ARG 0.005 0.000 ARG B 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 203 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: B 9 ASP cc_start: 0.7142 (m-30) cc_final: 0.6792 (m-30) REVERT: B 17 LYS cc_start: 0.7871 (mtmm) cc_final: 0.7616 (mtmm) REVERT: B 111 ASP cc_start: 0.7401 (t0) cc_final: 0.7128 (t0) REVERT: C 155 ASN cc_start: 0.7641 (p0) cc_final: 0.7382 (p0) REVERT: C 200 VAL cc_start: 0.8661 (m) cc_final: 0.8269 (p) REVERT: C 228 ASP cc_start: 0.6827 (OUTLIER) cc_final: 0.6353 (m-30) REVERT: C 234 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.7838 (m-80) REVERT: C 280 LYS cc_start: 0.8023 (tttp) cc_final: 0.7804 (tttp) REVERT: C 298 ASP cc_start: 0.7652 (t70) cc_final: 0.7399 (t70) REVERT: E 83 MET cc_start: 0.7863 (mtt) cc_final: 0.7502 (mtt) REVERT: E 128 MET cc_start: 0.7998 (ptt) cc_final: 0.7620 (ptm) REVERT: R 112 MET cc_start: 0.8141 (mmt) cc_final: 0.7425 (mmt) REVERT: R 122 LEU cc_start: 0.8612 (mm) cc_final: 0.8297 (mt) REVERT: R 129 TRP cc_start: 0.8263 (t60) cc_final: 0.7708 (t60) REVERT: R 213 ARG cc_start: 0.7340 (ttt180) cc_final: 0.7041 (ttt180) outliers start: 24 outliers final: 22 residues processed: 212 average time/residue: 0.2205 time to fit residues: 61.4236 Evaluate side-chains 227 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 203 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 264 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 62 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 93 optimal weight: 0.3980 chunk 9 optimal weight: 0.0980 chunk 56 optimal weight: 9.9990 chunk 86 optimal weight: 0.0270 chunk 24 optimal weight: 0.9980 chunk 82 optimal weight: 0.1980 chunk 2 optimal weight: 1.9990 chunk 42 optimal weight: 0.0170 chunk 81 optimal weight: 0.7980 overall best weight: 0.1476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.147154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.127779 restraints weight = 12051.043| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.37 r_work: 0.3470 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8140 Z= 0.131 Angle : 0.541 10.321 11091 Z= 0.268 Chirality : 0.040 0.260 1305 Planarity : 0.003 0.036 1399 Dihedral : 3.663 22.135 1173 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.17 % Allowed : 19.75 % Favored : 78.09 % 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: 0.81 (0.27), residues: 1061 helix: 2.39 (0.29), residues: 358 sheet: 0.32 (0.31), residues: 283 loop : -0.95 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.002 0.000 HIS E 35 PHE 0.028 0.001 PHE R 273 TYR 0.009 0.001 TYR E 178 ARG 0.005 0.000 ARG C 283 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 3918.55 seconds wall clock time: 69 minutes 55.48 seconds (4195.48 seconds total)