Starting phenix.real_space_refine on Wed Sep 17 10:03:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yrg_39542/09_2025/8yrg_39542.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yrg_39542/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8yrg_39542/09_2025/8yrg_39542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yrg_39542/09_2025/8yrg_39542.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yrg_39542/09_2025/8yrg_39542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yrg_39542/09_2025/8yrg_39542.map" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 8, 'ASP:plan': 8, 'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 5, 'ASN:plan1': 1} 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: {'GLU:plan': 5, 'ASP:plan': 6, 'GLN:plan1': 4, 'ARG:plan': 7, 'ASN:plan1': 1} 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, 'ARG:plan': 1, 'GLU:plan': 2, '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, 'PHE:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'TYR:plan': 1, 'ARG:plan': 4, 'GLU:plan': 2, 'ASP:plan': 1, 'HIS:plan': 2} 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: 1.81, per 1000 atoms: 0.23 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: 0.68 Conformation dependent library (CDL) restraints added in 453.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.29 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: 1.35 Time building geometry restraints manager: 0.94 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: 1.460 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.040 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.180 ------------------------------------------------------------------------------- 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 8142 Z= 0.302 Angle : 0.692 9.616 11095 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.011 0.001 ARG C 68 TYR 0.023 0.002 TYR R 106 PHE 0.024 0.002 PHE C 151 TRP 0.022 0.003 TRP C 339 HIS 0.009 0.002 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00687 ( 8140) covalent geometry : angle 0.69135 (11091) SS BOND : bond 0.00690 ( 2) SS BOND : angle 1.14554 ( 4) hydrogen bonds : bond 0.17018 ( 401) hydrogen bonds : angle 7.11967 ( 1149) *********************** 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 : 0.248 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: 0.1072 time to fit residues: 28.0723 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 : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.142704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.122667 restraints weight = 11989.136| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.39 r_work: 0.3399 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8142 Z= 0.172 Angle : 0.602 9.808 11095 Z= 0.310 Chirality : 0.043 0.181 1305 Planarity : 0.004 0.050 1399 Dihedral : 4.694 24.084 1173 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.15 % Allowed : 10.19 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.26), residues: 1061 helix: 1.24 (0.28), residues: 351 sheet: -0.22 (0.30), residues: 290 loop : -1.41 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 304 TYR 0.021 0.002 TYR R 106 PHE 0.015 0.002 PHE R 273 TRP 0.013 0.002 TRP C 63 HIS 0.005 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 8140) covalent geometry : angle 0.60155 (11091) SS BOND : bond 0.00721 ( 2) SS BOND : angle 1.25572 ( 4) hydrogen bonds : bond 0.04416 ( 401) hydrogen bonds : angle 5.13363 ( 1149) *********************** 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 224 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 215 time to evaluate : 0.281 Fit side-chains REVERT: B 9 ASP cc_start: 0.7146 (m-30) cc_final: 0.6804 (m-30) REVERT: B 95 LYS cc_start: 0.7786 (tppp) cc_final: 0.7199 (tppp) REVERT: B 130 ASN cc_start: 0.8510 (m-40) cc_final: 0.8289 (m-40) REVERT: C 118 ASP cc_start: 0.7099 (p0) cc_final: 0.6709 (p0) REVERT: C 135 VAL cc_start: 0.8175 (t) cc_final: 0.7905 (m) REVERT: C 155 ASN cc_start: 0.7656 (p0) cc_final: 0.7357 (p0) REVERT: C 204 CYS cc_start: 0.7634 (m) cc_final: 0.7433 (m) REVERT: C 277 SER cc_start: 0.8320 (t) cc_final: 0.7981 (p) REVERT: C 298 ASP cc_start: 0.7845 (t70) cc_final: 0.7468 (t70) REVERT: C 333 ASP cc_start: 0.7300 (p0) cc_final: 0.7098 (p0) REVERT: E 34 MET cc_start: 0.7998 (mmt) cc_final: 0.7763 (mmm) REVERT: E 218 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7540 (ttp) REVERT: R 223 LEU cc_start: 0.8225 (mp) cc_final: 0.7823 (mp) outliers start: 9 outliers final: 6 residues processed: 216 average time/residue: 0.1048 time to fit residues: 29.7575 Evaluate side-chains 220 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 213 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain R residue 155 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 93 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.142565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.123451 restraints weight = 11774.841| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.31 r_work: 0.3409 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8142 Z= 0.164 Angle : 0.582 10.266 11095 Z= 0.296 Chirality : 0.042 0.197 1305 Planarity : 0.004 0.047 1399 Dihedral : 4.430 23.143 1173 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.55 % Allowed : 12.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.26), residues: 1061 helix: 1.52 (0.28), residues: 352 sheet: -0.07 (0.30), residues: 294 loop : -1.40 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 283 TYR 0.018 0.002 TYR R 106 PHE 0.023 0.002 PHE R 273 TRP 0.013 0.002 TRP C 169 HIS 0.004 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8140) covalent geometry : angle 0.58152 (11091) SS BOND : bond 0.00697 ( 2) SS BOND : angle 1.18440 ( 4) hydrogen bonds : bond 0.04099 ( 401) hydrogen bonds : angle 4.84834 ( 1149) *********************** 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 229 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 209 time to evaluate : 0.308 Fit side-chains REVERT: B 9 ASP cc_start: 0.7128 (m-30) cc_final: 0.6784 (m-30) REVERT: B 25 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6293 (mp0) REVERT: B 95 LYS cc_start: 0.7794 (tppp) cc_final: 0.7196 (tppp) REVERT: C 118 ASP cc_start: 0.7060 (p0) cc_final: 0.6676 (p0) REVERT: C 135 VAL cc_start: 0.8140 (t) cc_final: 0.7886 (m) REVERT: C 155 ASN cc_start: 0.7656 (p0) cc_final: 0.7377 (p0) REVERT: C 298 ASP cc_start: 0.7784 (t70) cc_final: 0.7428 (t70) REVERT: E 34 MET cc_start: 0.7971 (mmt) cc_final: 0.7702 (mmm) REVERT: R 223 LEU cc_start: 0.8204 (mp) cc_final: 0.7800 (mp) outliers start: 20 outliers final: 17 residues processed: 215 average time/residue: 0.1094 time to fit residues: 30.7412 Evaluate side-chains 223 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 205 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain R residue 258 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 56 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 13 optimal weight: 0.0670 chunk 11 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.142373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.123178 restraints weight = 12081.676| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.33 r_work: 0.3405 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8142 Z= 0.174 Angle : 0.578 10.044 11095 Z= 0.295 Chirality : 0.043 0.217 1305 Planarity : 0.004 0.046 1399 Dihedral : 4.373 22.769 1173 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.44 % Allowed : 14.65 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.26), residues: 1061 helix: 1.60 (0.28), residues: 352 sheet: -0.05 (0.30), residues: 294 loop : -1.36 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 68 TYR 0.017 0.002 TYR E 178 PHE 0.024 0.002 PHE R 273 TRP 0.012 0.002 TRP C 169 HIS 0.004 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 8140) covalent geometry : angle 0.57759 (11091) SS BOND : bond 0.00709 ( 2) SS BOND : angle 1.25834 ( 4) hydrogen bonds : bond 0.03999 ( 401) hydrogen bonds : angle 4.75858 ( 1149) *********************** 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 230 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 203 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: B 9 ASP cc_start: 0.7143 (m-30) cc_final: 0.6796 (m-30) REVERT: C 118 ASP cc_start: 0.7062 (p0) cc_final: 0.6671 (p0) REVERT: C 135 VAL cc_start: 0.8133 (t) cc_final: 0.7889 (m) REVERT: C 137 ARG cc_start: 0.7278 (ttm-80) cc_final: 0.6995 (ttm-80) REVERT: C 155 ASN cc_start: 0.7655 (p0) cc_final: 0.7366 (p0) REVERT: C 298 ASP cc_start: 0.7773 (t70) cc_final: 0.7418 (t70) REVERT: R 223 LEU cc_start: 0.8212 (mp) cc_final: 0.7801 (mp) outliers start: 27 outliers final: 23 residues processed: 212 average time/residue: 0.1055 time to fit residues: 29.7146 Evaluate side-chains 225 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 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 263 THR Chi-restraints excluded: chain C residue 294 CYS 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 151 LEU Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 258 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 95 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 59 optimal weight: 0.1980 chunk 24 optimal weight: 0.9980 chunk 69 optimal weight: 0.2980 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3802 r_free = 0.3802 target = 0.142767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.123618 restraints weight = 11997.234| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.34 r_work: 0.3413 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8142 Z= 0.158 Angle : 0.576 10.596 11095 Z= 0.291 Chirality : 0.042 0.228 1305 Planarity : 0.004 0.044 1399 Dihedral : 4.291 23.195 1173 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.57 % Allowed : 14.90 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.26), residues: 1061 helix: 1.76 (0.28), residues: 352 sheet: -0.02 (0.30), residues: 294 loop : -1.31 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 68 TYR 0.016 0.001 TYR E 178 PHE 0.026 0.002 PHE R 273 TRP 0.011 0.002 TRP C 63 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 8140) covalent geometry : angle 0.57526 (11091) SS BOND : bond 0.00707 ( 2) SS BOND : angle 1.15487 ( 4) hydrogen bonds : bond 0.03825 ( 401) hydrogen bonds : angle 4.65289 ( 1149) *********************** 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 232 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 0.583 Fit side-chains revert: symmetry clash REVERT: B 9 ASP cc_start: 0.7144 (m-30) cc_final: 0.6805 (m-30) REVERT: C 118 ASP cc_start: 0.7024 (p0) cc_final: 0.6671 (p0) REVERT: C 135 VAL cc_start: 0.8124 (t) cc_final: 0.7914 (m) REVERT: C 137 ARG cc_start: 0.7293 (ttm-80) cc_final: 0.7016 (ttm-80) REVERT: C 155 ASN cc_start: 0.7640 (p0) cc_final: 0.7367 (p0) REVERT: C 200 VAL cc_start: 0.8703 (m) cc_final: 0.8355 (p) REVERT: C 298 ASP cc_start: 0.7769 (t70) cc_final: 0.7411 (t70) REVERT: C 333 ASP cc_start: 0.7112 (p0) cc_final: 0.6907 (p0) REVERT: E 83 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.6855 (mmt) REVERT: R 129 TRP cc_start: 0.8309 (t60) cc_final: 0.7859 (t60) REVERT: R 223 LEU cc_start: 0.8214 (mp) cc_final: 0.7804 (mp) outliers start: 28 outliers final: 19 residues processed: 213 average time/residue: 0.1047 time to fit residues: 29.5841 Evaluate side-chains 223 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 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 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 258 MET 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 3 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 76 optimal weight: 0.2980 chunk 18 optimal weight: 0.4980 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3802 r_free = 0.3802 target = 0.142931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.123806 restraints weight = 11989.164| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.33 r_work: 0.3411 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8142 Z= 0.159 Angle : 0.579 10.173 11095 Z= 0.293 Chirality : 0.042 0.243 1305 Planarity : 0.004 0.041 1399 Dihedral : 4.222 23.531 1173 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.95 % Allowed : 15.41 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.26), residues: 1061 helix: 1.80 (0.28), residues: 353 sheet: 0.02 (0.30), residues: 293 loop : -1.31 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 68 TYR 0.017 0.001 TYR E 178 PHE 0.027 0.002 PHE R 273 TRP 0.011 0.002 TRP C 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 8140) covalent geometry : angle 0.57830 (11091) SS BOND : bond 0.00699 ( 2) SS BOND : angle 1.11276 ( 4) hydrogen bonds : bond 0.03781 ( 401) hydrogen bonds : angle 4.55577 ( 1149) *********************** 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 236 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: B 9 ASP cc_start: 0.7147 (m-30) cc_final: 0.6789 (m-30) REVERT: C 118 ASP cc_start: 0.7040 (p0) cc_final: 0.6648 (p0) REVERT: C 137 ARG cc_start: 0.7282 (ttm-80) cc_final: 0.7008 (ttm-80) REVERT: C 155 ASN cc_start: 0.7630 (p0) cc_final: 0.7351 (p0) REVERT: C 200 VAL cc_start: 0.8704 (m) cc_final: 0.8329 (p) REVERT: C 228 ASP cc_start: 0.6826 (OUTLIER) cc_final: 0.6485 (m-30) REVERT: C 259 GLN cc_start: 0.8231 (tt0) cc_final: 0.8019 (tt0) REVERT: C 298 ASP cc_start: 0.7760 (t70) cc_final: 0.7402 (t70) REVERT: E 128 MET cc_start: 0.8119 (ptt) cc_final: 0.7846 (ptm) REVERT: R 129 TRP cc_start: 0.8305 (t60) cc_final: 0.7866 (t60) REVERT: R 223 LEU cc_start: 0.8211 (mp) cc_final: 0.7817 (mp) outliers start: 31 outliers final: 23 residues processed: 217 average time/residue: 0.1043 time to fit residues: 30.0650 Evaluate side-chains 226 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 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 294 CYS 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 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 258 MET 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 76 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 102 optimal weight: 0.0010 chunk 31 optimal weight: 0.0370 chunk 105 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.4064 ------------------------------------------------------------------------------- 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 = 0.144290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.124924 restraints weight = 12004.484| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.35 r_work: 0.3431 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8142 Z= 0.120 Angle : 0.552 10.491 11095 Z= 0.280 Chirality : 0.041 0.253 1305 Planarity : 0.003 0.039 1399 Dihedral : 4.032 24.370 1173 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.80 % Allowed : 17.58 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.27), residues: 1061 helix: 2.03 (0.29), residues: 353 sheet: 0.12 (0.30), residues: 294 loop : -1.26 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 283 TYR 0.013 0.001 TYR E 178 PHE 0.028 0.001 PHE R 273 TRP 0.011 0.001 TRP C 63 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8140) covalent geometry : angle 0.55173 (11091) SS BOND : bond 0.00567 ( 2) SS BOND : angle 0.90417 ( 4) hydrogen bonds : bond 0.03432 ( 401) hydrogen bonds : angle 4.44440 ( 1149) *********************** 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 228 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: C 155 ASN cc_start: 0.7633 (p0) cc_final: 0.7369 (p0) REVERT: C 200 VAL cc_start: 0.8668 (m) cc_final: 0.8315 (p) REVERT: C 228 ASP cc_start: 0.6829 (OUTLIER) cc_final: 0.6358 (m-30) REVERT: C 298 ASP cc_start: 0.7710 (t70) cc_final: 0.7379 (t70) REVERT: E 83 MET cc_start: 0.7820 (mtm) cc_final: 0.7452 (mtt) REVERT: R 112 MET cc_start: 0.8187 (mmt) cc_final: 0.7637 (mmt) REVERT: R 129 TRP cc_start: 0.8263 (t60) cc_final: 0.7746 (t60) REVERT: R 223 LEU cc_start: 0.8210 (mp) cc_final: 0.7817 (mp) outliers start: 22 outliers final: 19 residues processed: 214 average time/residue: 0.1029 time to fit residues: 29.0829 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 : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU 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 228 ASP 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 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 258 MET 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 87 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 93 optimal weight: 0.0040 chunk 2 optimal weight: 0.9980 chunk 96 optimal weight: 0.0010 chunk 65 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.144123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.124885 restraints weight = 11942.096| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.33 r_work: 0.3427 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8142 Z= 0.140 Angle : 0.585 10.825 11095 Z= 0.292 Chirality : 0.042 0.254 1305 Planarity : 0.003 0.039 1399 Dihedral : 4.072 24.166 1173 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.31 % Allowed : 18.85 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.27), residues: 1061 helix: 2.04 (0.29), residues: 353 sheet: 0.11 (0.30), residues: 295 loop : -1.20 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 68 TYR 0.016 0.001 TYR E 178 PHE 0.027 0.001 PHE R 273 TRP 0.011 0.001 TRP C 169 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8140) covalent geometry : angle 0.58450 (11091) SS BOND : bond 0.00622 ( 2) SS BOND : angle 0.96182 ( 4) hydrogen bonds : bond 0.03564 ( 401) hydrogen bonds : angle 4.44173 ( 1149) *********************** 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 227 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 201 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: B 9 ASP cc_start: 0.7122 (m-30) cc_final: 0.6772 (m-30) REVERT: C 155 ASN cc_start: 0.7642 (p0) cc_final: 0.7383 (p0) REVERT: C 188 MET cc_start: 0.7687 (mtp) cc_final: 0.7401 (mtp) REVERT: C 200 VAL cc_start: 0.8668 (m) cc_final: 0.8263 (p) REVERT: C 228 ASP cc_start: 0.6813 (OUTLIER) cc_final: 0.6483 (m-30) REVERT: C 234 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.7872 (m-80) REVERT: C 298 ASP cc_start: 0.7692 (t70) cc_final: 0.7365 (t70) REVERT: E 83 MET cc_start: 0.7953 (mtm) cc_final: 0.7648 (mtt) REVERT: E 128 MET cc_start: 0.8003 (ptt) cc_final: 0.7697 (ptm) REVERT: R 112 MET cc_start: 0.8204 (mmt) cc_final: 0.7648 (mmt) REVERT: R 129 TRP cc_start: 0.8263 (t60) cc_final: 0.7751 (t60) REVERT: R 223 LEU cc_start: 0.8223 (mp) cc_final: 0.7827 (mp) outliers start: 26 outliers final: 22 residues processed: 211 average time/residue: 0.1041 time to fit residues: 29.0420 Evaluate side-chains 225 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 201 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain C residue 114 CYS 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 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 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 258 MET 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 9 optimal weight: 0.7980 chunk 65 optimal weight: 0.0040 chunk 89 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.2980 chunk 77 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 chunk 11 optimal weight: 0.0980 overall best weight: 0.2992 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.145181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.126040 restraints weight = 11964.284| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.34 r_work: 0.3448 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8142 Z= 0.109 Angle : 0.552 10.818 11095 Z= 0.276 Chirality : 0.041 0.259 1305 Planarity : 0.003 0.037 1399 Dihedral : 3.881 23.077 1173 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.42 % Allowed : 19.62 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.27), residues: 1061 helix: 2.20 (0.29), residues: 358 sheet: 0.25 (0.31), residues: 294 loop : -1.11 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 283 TYR 0.013 0.001 TYR E 178 PHE 0.026 0.001 PHE R 273 TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 8140) covalent geometry : angle 0.55141 (11091) SS BOND : bond 0.00573 ( 2) SS BOND : angle 0.87017 ( 4) hydrogen bonds : bond 0.03180 ( 401) hydrogen bonds : angle 4.32410 ( 1149) *********************** 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 222 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: C 155 ASN cc_start: 0.7630 (p0) cc_final: 0.7376 (p0) REVERT: C 188 MET cc_start: 0.7708 (mtp) cc_final: 0.7415 (mtp) REVERT: C 200 VAL cc_start: 0.8650 (m) cc_final: 0.8270 (p) REVERT: C 228 ASP cc_start: 0.6839 (OUTLIER) cc_final: 0.6401 (m-30) REVERT: C 234 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.7825 (m-80) REVERT: C 251 ARG cc_start: 0.7955 (mtt-85) cc_final: 0.7556 (mtt-85) REVERT: C 280 LYS cc_start: 0.8004 (tttp) cc_final: 0.7796 (tttp) REVERT: C 298 ASP cc_start: 0.7638 (t70) cc_final: 0.7249 (t70) REVERT: E 83 MET cc_start: 0.7920 (mtm) cc_final: 0.7648 (mtt) REVERT: R 74 LEU cc_start: 0.7678 (tp) cc_final: 0.7238 (mp) REVERT: R 95 ARG cc_start: 0.7810 (mtt180) cc_final: 0.7548 (mtt180) REVERT: R 112 MET cc_start: 0.8184 (mmt) cc_final: 0.7683 (mmt) REVERT: R 122 LEU cc_start: 0.8606 (mm) cc_final: 0.8279 (mt) REVERT: R 129 TRP cc_start: 0.8241 (t60) cc_final: 0.7681 (t60) REVERT: R 213 ARG cc_start: 0.7302 (ttt180) cc_final: 0.7001 (ttt180) REVERT: R 223 LEU cc_start: 0.8196 (mp) cc_final: 0.7809 (mp) outliers start: 19 outliers final: 13 residues processed: 214 average time/residue: 0.1028 time to fit residues: 28.9619 Evaluate side-chains 215 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 200 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 122 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 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 116 ILE Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 253 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 103 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 39 optimal weight: 0.0170 chunk 16 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.6822 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.143816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.124682 restraints weight = 11931.541| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.33 r_work: 0.3421 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8142 Z= 0.161 Angle : 0.601 10.971 11095 Z= 0.299 Chirality : 0.042 0.255 1305 Planarity : 0.003 0.039 1399 Dihedral : 4.082 22.797 1173 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.42 % Allowed : 19.24 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.27), residues: 1061 helix: 2.11 (0.28), residues: 353 sheet: 0.09 (0.30), residues: 297 loop : -1.06 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 68 TYR 0.018 0.001 TYR E 178 PHE 0.025 0.002 PHE R 273 TRP 0.011 0.002 TRP C 169 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 8140) covalent geometry : angle 0.60061 (11091) SS BOND : bond 0.00670 ( 2) SS BOND : angle 1.01374 ( 4) hydrogen bonds : bond 0.03689 ( 401) hydrogen bonds : angle 4.41239 ( 1149) ********************** 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 223 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 204 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: B 9 ASP cc_start: 0.7178 (m-30) cc_final: 0.6809 (m-30) REVERT: C 155 ASN cc_start: 0.7636 (p0) cc_final: 0.7381 (p0) REVERT: C 188 MET cc_start: 0.7678 (mtp) cc_final: 0.7392 (mtp) REVERT: C 200 VAL cc_start: 0.8684 (m) cc_final: 0.8281 (p) REVERT: C 228 ASP cc_start: 0.6809 (OUTLIER) cc_final: 0.6472 (m-30) REVERT: C 234 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.7871 (m-80) REVERT: C 298 ASP cc_start: 0.7672 (t70) cc_final: 0.7362 (t70) REVERT: E 83 MET cc_start: 0.7922 (mtm) cc_final: 0.7658 (mtt) REVERT: E 128 MET cc_start: 0.8005 (ptt) cc_final: 0.7622 (ptm) REVERT: R 112 MET cc_start: 0.8217 (mmt) cc_final: 0.7611 (mmt) REVERT: R 122 LEU cc_start: 0.8642 (mm) cc_final: 0.8391 (mt) REVERT: R 129 TRP cc_start: 0.8272 (t60) cc_final: 0.7758 (t60) REVERT: R 213 ARG cc_start: 0.7337 (ttt180) cc_final: 0.7037 (ttt180) REVERT: R 223 LEU cc_start: 0.8199 (mp) cc_final: 0.7820 (mp) outliers start: 19 outliers final: 16 residues processed: 214 average time/residue: 0.1013 time to fit residues: 28.7519 Evaluate side-chains 219 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 201 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 122 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 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 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 12 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 0.1980 chunk 19 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 96 optimal weight: 0.0870 overall best weight: 0.6360 ------------------------------------------------------------------------------- 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 = 0.3818 r_free = 0.3818 target = 0.144014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.124901 restraints weight = 11954.030| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.33 r_work: 0.3427 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8142 Z= 0.153 Angle : 0.601 11.302 11095 Z= 0.297 Chirality : 0.042 0.255 1305 Planarity : 0.003 0.039 1399 Dihedral : 4.094 24.029 1173 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.55 % Allowed : 19.62 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.27), residues: 1061 helix: 2.14 (0.28), residues: 352 sheet: 0.12 (0.30), residues: 295 loop : -1.09 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 68 TYR 0.017 0.001 TYR E 178 PHE 0.024 0.001 PHE R 273 TRP 0.061 0.002 TRP R 158 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8140) covalent geometry : angle 0.60046 (11091) SS BOND : bond 0.00664 ( 2) SS BOND : angle 0.97282 ( 4) hydrogen bonds : bond 0.03629 ( 401) hydrogen bonds : angle 4.42157 ( 1149) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2029.79 seconds wall clock time: 35 minutes 13.47 seconds (2113.47 seconds total)