Starting phenix.real_space_refine on Wed Mar 12 13:32:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yrg_39542/03_2025/8yrg_39542.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yrg_39542/03_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_39542/03_2025/8yrg_39542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yrg_39542/03_2025/8yrg_39542.map" model { file = "/net/cci-nas-00/data/ceres_data/8yrg_39542/03_2025/8yrg_39542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yrg_39542/03_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-5624/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: 5.32, per 1000 atoms: 0.67 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: 2.12 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.90 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: 2.26 Time building geometry restraints manager: 2.45 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.960 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.920 ------------------------------------------------------------------------------- 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 : 0.831 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: 0.2241 time to fit residues: 58.6492 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 : 0.820 ------------------------------------------------------------------------------- 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: 0.5980 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 0.0570 overall best weight: 0.6300 ------------------------------------------------------------------------------- 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 = 0.142995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.123024 restraints weight = 11848.324| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.37 r_work: 0.3405 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.0980 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= 0.233 Angle : 0.595 9.702 11091 Z= 0.307 Chirality : 0.043 0.171 1305 Planarity : 0.004 0.049 1399 Dihedral : 4.665 24.650 1173 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.02 % Allowed : 10.57 % 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: 351 sheet: -0.20 (0.30), residues: 290 loop : -1.39 (0.30), residues: 420 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 222 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 214 time to evaluate : 0.867 Fit side-chains REVERT: B 9 ASP cc_start: 0.7146 (m-30) cc_final: 0.6812 (m-30) REVERT: B 95 LYS cc_start: 0.7784 (tppp) cc_final: 0.7191 (tppp) REVERT: B 130 ASN cc_start: 0.8509 (m-40) cc_final: 0.8287 (m-40) REVERT: C 118 ASP cc_start: 0.7094 (p0) cc_final: 0.6703 (p0) REVERT: C 135 VAL cc_start: 0.8167 (t) cc_final: 0.7892 (m) REVERT: C 155 ASN cc_start: 0.7675 (p0) cc_final: 0.7373 (p0) REVERT: C 204 CYS cc_start: 0.7642 (m) cc_final: 0.7424 (m) REVERT: C 251 ARG cc_start: 0.8101 (mtt-85) cc_final: 0.7771 (mtt-85) REVERT: C 277 SER cc_start: 0.8316 (t) cc_final: 0.7977 (p) REVERT: C 298 ASP cc_start: 0.7813 (t70) cc_final: 0.7429 (t70) REVERT: C 333 ASP cc_start: 0.7301 (p0) cc_final: 0.7101 (p0) REVERT: E 34 MET cc_start: 0.8000 (mmt) cc_final: 0.7769 (mmm) REVERT: R 223 LEU cc_start: 0.8233 (mp) cc_final: 0.7826 (mp) outliers start: 8 outliers final: 7 residues processed: 214 average time/residue: 0.2243 time to fit residues: 62.9983 Evaluate side-chains 219 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 212 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 62 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 32 optimal weight: 0.0770 chunk 54 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 = 0.143498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.124265 restraints weight = 12010.023| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.33 r_work: 0.3417 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.1326 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= 0.200 Angle : 0.558 9.985 11091 Z= 0.284 Chirality : 0.042 0.196 1305 Planarity : 0.004 0.045 1399 Dihedral : 4.298 23.435 1173 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.55 % Allowed : 12.99 % Favored : 84.46 % 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: 1.67 (0.29), residues: 352 sheet: 0.04 (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 0.022 0.001 PHE R 273 TYR 0.015 0.001 TYR R 106 ARG 0.004 0.000 ARG B 15 *********************** 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 230 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 210 time to evaluate : 0.829 Fit side-chains REVERT: B 17 LYS cc_start: 0.7879 (mtmm) cc_final: 0.7619 (mtmm) REVERT: B 25 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6306 (mp0) REVERT: B 95 LYS cc_start: 0.7754 (tppp) cc_final: 0.7165 (tppp) REVERT: C 135 VAL cc_start: 0.8131 (t) cc_final: 0.7885 (m) REVERT: C 155 ASN cc_start: 0.7657 (p0) cc_final: 0.7375 (p0) REVERT: C 298 ASP cc_start: 0.7747 (t70) cc_final: 0.7407 (t70) REVERT: E 34 MET cc_start: 0.7968 (mmt) cc_final: 0.7735 (mmm) REVERT: R 223 LEU cc_start: 0.8195 (mp) cc_final: 0.7787 (mp) outliers start: 20 outliers final: 15 residues processed: 216 average time/residue: 0.2219 time to fit residues: 63.0729 Evaluate side-chains 222 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 206 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 49 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 72 optimal weight: 0.4980 chunk 84 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.142724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.123698 restraints weight = 11920.385| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.31 r_work: 0.3412 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8140 Z= 0.252 Angle : 0.576 9.794 11091 Z= 0.292 Chirality : 0.042 0.213 1305 Planarity : 0.004 0.045 1399 Dihedral : 4.325 22.185 1173 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.06 % Allowed : 14.78 % Favored : 82.17 % 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: 0.10 (0.26), residues: 1061 helix: 1.71 (0.28), residues: 352 sheet: 0.05 (0.30), residues: 292 loop : -1.36 (0.30), residues: 417 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 0.017 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 230 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: B 9 ASP cc_start: 0.7135 (m-30) cc_final: 0.6791 (m-30) REVERT: C 118 ASP cc_start: 0.7045 (p0) cc_final: 0.6655 (p0) REVERT: C 135 VAL cc_start: 0.8134 (t) cc_final: 0.7894 (m) REVERT: C 155 ASN cc_start: 0.7622 (p0) cc_final: 0.7333 (p0) REVERT: C 298 ASP cc_start: 0.7763 (t70) cc_final: 0.7410 (t70) REVERT: R 112 MET cc_start: 0.8147 (mmt) cc_final: 0.7510 (mmt) REVERT: R 129 TRP cc_start: 0.8280 (t60) cc_final: 0.7846 (t60) REVERT: R 223 LEU cc_start: 0.8205 (mp) cc_final: 0.7789 (mp) outliers start: 24 outliers final: 18 residues processed: 215 average time/residue: 0.2243 time to fit residues: 63.7240 Evaluate side-chains 228 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 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 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 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: 0.5980 chunk 46 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 80 optimal weight: 0.0170 chunk 9 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 100 optimal weight: 0.0970 chunk 30 optimal weight: 0.7980 chunk 10 optimal weight: 0.0980 overall best weight: 0.3216 ------------------------------------------------------------------------------- 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 = 0.3826 r_free = 0.3826 target = 0.144673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.125634 restraints weight = 11858.137| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.31 r_work: 0.3436 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8140 Z= 0.156 Angle : 0.536 10.079 11091 Z= 0.270 Chirality : 0.041 0.227 1305 Planarity : 0.003 0.040 1399 Dihedral : 4.021 23.620 1173 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.68 % Allowed : 15.92 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.27), residues: 1061 helix: 2.05 (0.29), residues: 353 sheet: 0.19 (0.30), residues: 292 loop : -1.26 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.027 0.001 PHE R 273 TYR 0.012 0.001 TYR E 178 ARG 0.004 0.000 ARG B 15 *********************** 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: 21 poor density : 215 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.7852 (mtmm) cc_final: 0.7566 (mtmm) REVERT: C 155 ASN cc_start: 0.7637 (p0) cc_final: 0.7361 (p0) REVERT: C 200 VAL cc_start: 0.8681 (m) cc_final: 0.8349 (p) REVERT: C 228 ASP cc_start: 0.6829 (OUTLIER) cc_final: 0.6393 (m-30) REVERT: C 263 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8228 (t) REVERT: C 298 ASP cc_start: 0.7674 (t70) cc_final: 0.7365 (t70) REVERT: E 34 MET cc_start: 0.7888 (mmt) cc_final: 0.7609 (mmm) REVERT: E 83 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.6893 (mmt) REVERT: E 128 MET cc_start: 0.8088 (ptm) cc_final: 0.7876 (ptp) REVERT: R 74 LEU cc_start: 0.7691 (tp) cc_final: 0.7277 (mp) REVERT: R 112 MET cc_start: 0.8142 (mmt) cc_final: 0.7493 (mmt) REVERT: R 129 TRP cc_start: 0.8248 (t60) cc_final: 0.7673 (t60) REVERT: R 223 LEU cc_start: 0.8196 (mp) cc_final: 0.7800 (mp) outliers start: 21 outliers final: 13 residues processed: 222 average time/residue: 0.2116 time to fit residues: 62.5707 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 : 0.870 ------------------------------------------------------------------------------- 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 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 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 R residue 114 SER Chi-restraints excluded: chain R residue 151 LEU 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 25 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 72 optimal weight: 0.0980 chunk 1 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.142331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.123214 restraints weight = 11906.375| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.31 r_work: 0.3405 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8140 Z= 0.298 Angle : 0.607 10.649 11091 Z= 0.305 Chirality : 0.043 0.236 1305 Planarity : 0.004 0.041 1399 Dihedral : 4.303 23.636 1173 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.69 % Allowed : 15.29 % Favored : 81.02 % 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: 0.24 (0.26), residues: 1061 helix: 1.83 (0.28), residues: 353 sheet: 0.11 (0.30), residues: 293 loop : -1.27 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 169 HIS 0.005 0.001 HIS B 214 PHE 0.024 0.002 PHE R 273 TYR 0.020 0.002 TYR E 178 ARG 0.005 0.000 ARG C 68 *********************** 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 234 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 205 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: B 9 ASP cc_start: 0.7176 (m-30) cc_final: 0.6824 (m-30) REVERT: B 17 LYS cc_start: 0.7864 (mtmm) cc_final: 0.7604 (mtmm) REVERT: C 118 ASP cc_start: 0.7064 (p0) cc_final: 0.6679 (p0) REVERT: C 137 ARG cc_start: 0.7313 (ttm-80) cc_final: 0.7017 (ttm-80) REVERT: C 155 ASN cc_start: 0.7634 (p0) cc_final: 0.7359 (p0) REVERT: C 200 VAL cc_start: 0.8678 (m) cc_final: 0.8311 (p) REVERT: C 259 GLN cc_start: 0.8218 (tt0) cc_final: 0.8010 (tt0) REVERT: C 298 ASP cc_start: 0.7728 (t70) cc_final: 0.7396 (t70) REVERT: E 83 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.6973 (mmt) REVERT: R 112 MET cc_start: 0.8185 (mmt) cc_final: 0.7570 (mmt) REVERT: R 129 TRP cc_start: 0.8286 (t60) cc_final: 0.7841 (t60) REVERT: R 223 LEU cc_start: 0.8210 (mp) cc_final: 0.7817 (mp) outliers start: 29 outliers final: 25 residues processed: 218 average time/residue: 0.2097 time to fit residues: 61.1539 Evaluate side-chains 229 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 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 246 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 0.0060 chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 22 optimal weight: 9.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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 = 0.143965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.124677 restraints weight = 12006.774| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.35 r_work: 0.3422 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.1814 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= 0.180 Angle : 0.557 10.137 11091 Z= 0.279 Chirality : 0.041 0.251 1305 Planarity : 0.003 0.038 1399 Dihedral : 4.074 25.451 1173 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.57 % Allowed : 16.69 % Favored : 79.75 % 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: 0.44 (0.27), residues: 1061 helix: 2.08 (0.29), residues: 353 sheet: 0.16 (0.30), residues: 294 loop : -1.21 (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 0.020 0.001 PHE R 273 TYR 0.014 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 230 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.7856 (mtmm) cc_final: 0.7628 (mtmm) REVERT: B 111 ASP cc_start: 0.7396 (t0) cc_final: 0.7146 (t0) REVERT: B 230 ASP cc_start: 0.6756 (m-30) cc_final: 0.6430 (m-30) REVERT: C 155 ASN cc_start: 0.7626 (p0) cc_final: 0.7357 (p0) REVERT: C 200 VAL cc_start: 0.8695 (m) cc_final: 0.8286 (p) REVERT: C 228 ASP cc_start: 0.6828 (OUTLIER) cc_final: 0.6354 (m-30) REVERT: C 234 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.7881 (m-80) REVERT: C 298 ASP cc_start: 0.7679 (t70) cc_final: 0.7404 (t70) REVERT: E 34 MET cc_start: 0.7948 (mmt) cc_final: 0.7672 (mmm) REVERT: E 128 MET cc_start: 0.8215 (ptp) cc_final: 0.7937 (ptm) REVERT: R 112 MET cc_start: 0.8159 (mmt) cc_final: 0.7421 (mmt) REVERT: R 129 TRP cc_start: 0.8261 (t60) cc_final: 0.7751 (t60) REVERT: R 223 LEU cc_start: 0.8203 (mp) cc_final: 0.7808 (mp) outliers start: 28 outliers final: 20 residues processed: 216 average time/residue: 0.2073 time to fit residues: 59.5458 Evaluate side-chains 224 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 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 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 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 102 optimal weight: 0.0770 chunk 39 optimal weight: 0.0010 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 overall best weight: 0.3944 ------------------------------------------------------------------------------- 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 = 0.144690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.125509 restraints weight = 11969.743| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.34 r_work: 0.3437 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.1975 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= 0.171 Angle : 0.561 10.325 11091 Z= 0.279 Chirality : 0.041 0.256 1305 Planarity : 0.003 0.037 1399 Dihedral : 3.962 26.021 1173 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.31 % Allowed : 17.83 % Favored : 78.85 % 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: 0.54 (0.27), residues: 1061 helix: 2.17 (0.29), residues: 353 sheet: 0.23 (0.31), residues: 294 loop : -1.15 (0.31), residues: 414 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 0.027 0.001 PHE R 273 TYR 0.015 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 234 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 0.868 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.7845 (mtmm) cc_final: 0.7596 (mtmm) REVERT: B 111 ASP cc_start: 0.7410 (t0) cc_final: 0.7151 (t0) REVERT: C 155 ASN cc_start: 0.7634 (p0) cc_final: 0.7364 (p0) REVERT: C 200 VAL cc_start: 0.8691 (m) cc_final: 0.8263 (p) REVERT: C 228 ASP cc_start: 0.6811 (OUTLIER) cc_final: 0.6356 (m-30) REVERT: C 234 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.7821 (m-80) REVERT: C 280 LYS cc_start: 0.8030 (tttp) cc_final: 0.7813 (tttp) REVERT: C 298 ASP cc_start: 0.7652 (t70) cc_final: 0.7394 (t70) REVERT: E 34 MET cc_start: 0.7938 (mmt) cc_final: 0.7656 (mmm) REVERT: E 83 MET cc_start: 0.7815 (mtm) cc_final: 0.7497 (mtt) REVERT: R 74 LEU cc_start: 0.7713 (tp) cc_final: 0.7290 (mp) REVERT: R 95 ARG cc_start: 0.7825 (mtt180) cc_final: 0.7562 (mtt180) REVERT: R 112 MET cc_start: 0.8130 (mmt) cc_final: 0.7441 (mmt) REVERT: R 129 TRP cc_start: 0.8249 (t60) cc_final: 0.7721 (t60) REVERT: R 223 LEU cc_start: 0.8196 (mp) cc_final: 0.7807 (mp) outliers start: 26 outliers final: 22 residues processed: 220 average time/residue: 0.2153 time to fit residues: 62.7422 Evaluate side-chains 230 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 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 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 0 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 75 optimal weight: 0.2980 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 0.4980 chunk 96 optimal weight: 0.0000 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 overall best weight: 0.4184 ------------------------------------------------------------------------------- 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 = 0.3829 r_free = 0.3829 target = 0.144930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.125497 restraints weight = 12051.375| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.38 r_work: 0.3432 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.2036 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= 0.175 Angle : 0.565 10.596 11091 Z= 0.280 Chirality : 0.041 0.257 1305 Planarity : 0.003 0.038 1399 Dihedral : 3.928 25.220 1173 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.31 % Allowed : 18.22 % 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: 0.60 (0.27), residues: 1061 helix: 2.12 (0.29), residues: 359 sheet: 0.25 (0.31), residues: 294 loop : -1.05 (0.31), residues: 408 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 0.025 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 : 0.813 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.7846 (mtmm) cc_final: 0.7593 (mtmm) REVERT: B 21 LYS cc_start: 0.7639 (ttpp) cc_final: 0.7397 (ttpp) REVERT: B 111 ASP cc_start: 0.7407 (t0) cc_final: 0.7146 (t0) REVERT: C 61 MET cc_start: 0.7642 (ppp) cc_final: 0.7377 (ppp) REVERT: C 155 ASN cc_start: 0.7632 (p0) cc_final: 0.7382 (p0) REVERT: C 188 MET cc_start: 0.7690 (mtp) cc_final: 0.7406 (mtp) REVERT: C 200 VAL cc_start: 0.8658 (m) cc_final: 0.8248 (p) REVERT: C 228 ASP cc_start: 0.6812 (OUTLIER) cc_final: 0.6368 (m-30) REVERT: C 234 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.7835 (m-80) REVERT: C 280 LYS cc_start: 0.8029 (tttp) cc_final: 0.7812 (tttp) REVERT: C 298 ASP cc_start: 0.7639 (t70) cc_final: 0.7380 (t70) REVERT: E 34 MET cc_start: 0.7954 (mmt) cc_final: 0.7674 (mmm) REVERT: E 83 MET cc_start: 0.7667 (mtm) cc_final: 0.7279 (mtt) REVERT: R 74 LEU cc_start: 0.7709 (tp) cc_final: 0.7273 (mp) REVERT: R 95 ARG cc_start: 0.7844 (mtt180) cc_final: 0.7576 (mtt180) REVERT: R 112 MET cc_start: 0.8152 (mmt) cc_final: 0.7454 (mmt) REVERT: R 129 TRP cc_start: 0.8256 (t60) cc_final: 0.7674 (t60) REVERT: R 213 ARG cc_start: 0.7347 (ttt180) cc_final: 0.7034 (ttt180) REVERT: R 223 LEU cc_start: 0.8205 (mp) cc_final: 0.7824 (mp) outliers start: 26 outliers final: 23 residues processed: 214 average time/residue: 0.2126 time to fit residues: 59.8527 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 : 0.942 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- 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: 0.0970 chunk 20 optimal weight: 0.0870 chunk 57 optimal weight: 0.0370 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 72 optimal weight: 0.2980 chunk 50 optimal weight: 0.9990 overall best weight: 0.2034 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.146591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.127288 restraints weight = 11938.659| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.36 r_work: 0.3465 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8140 Z= 0.136 Angle : 0.541 10.130 11091 Z= 0.268 Chirality : 0.040 0.259 1305 Planarity : 0.003 0.036 1399 Dihedral : 3.692 24.452 1173 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.55 % Allowed : 19.24 % Favored : 78.22 % 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: 0.76 (0.27), residues: 1061 helix: 2.33 (0.29), residues: 358 sheet: 0.31 (0.31), residues: 283 loop : -0.98 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.024 0.001 PHE R 273 TYR 0.012 0.001 TYR E 178 ARG 0.005 0.000 ARG C 283 ********************** 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 222 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 LYS cc_start: 0.7855 (mtmm) cc_final: 0.7611 (mtmm) REVERT: B 21 LYS cc_start: 0.7669 (ttpp) cc_final: 0.7425 (ttpp) REVERT: B 111 ASP cc_start: 0.7409 (t0) cc_final: 0.7137 (t0) REVERT: B 240 LEU cc_start: 0.7821 (pp) cc_final: 0.7579 (tt) REVERT: C 124 TYR cc_start: 0.8005 (m-80) cc_final: 0.7761 (m-80) REVERT: C 155 ASN cc_start: 0.7649 (p0) cc_final: 0.7380 (p0) REVERT: C 200 VAL cc_start: 0.8665 (m) cc_final: 0.8287 (p) REVERT: C 228 ASP cc_start: 0.6864 (OUTLIER) cc_final: 0.6415 (m-30) REVERT: C 234 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.7740 (m-80) REVERT: C 280 LYS cc_start: 0.8010 (tttp) cc_final: 0.7807 (tttp) REVERT: E 34 MET cc_start: 0.7884 (mmt) cc_final: 0.7645 (mmm) REVERT: E 83 MET cc_start: 0.7638 (mtm) cc_final: 0.7283 (mtt) REVERT: R 74 LEU cc_start: 0.7679 (tp) cc_final: 0.7299 (mt) REVERT: R 95 ARG cc_start: 0.7788 (mtt180) cc_final: 0.7505 (mtt180) REVERT: R 112 MET cc_start: 0.8086 (mmt) cc_final: 0.7475 (mmt) REVERT: R 122 LEU cc_start: 0.8590 (mm) cc_final: 0.8313 (mt) REVERT: R 129 TRP cc_start: 0.8193 (t60) cc_final: 0.7569 (t60) REVERT: R 213 ARG cc_start: 0.7318 (ttt180) cc_final: 0.7017 (ttt180) outliers start: 20 outliers final: 15 residues processed: 211 average time/residue: 0.2127 time to fit residues: 58.9926 Evaluate side-chains 221 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 204 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 135 VAL 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 62 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 56 optimal weight: 6.9990 chunk 86 optimal weight: 0.0060 chunk 24 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 42 optimal weight: 0.0050 chunk 81 optimal weight: 0.9980 overall best weight: 0.4010 ------------------------------------------------------------------------------- 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 = 0.3846 r_free = 0.3846 target = 0.146211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.126796 restraints weight = 12051.299| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.36 r_work: 0.3447 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2274 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= 0.171 Angle : 0.553 10.141 11091 Z= 0.275 Chirality : 0.041 0.255 1305 Planarity : 0.003 0.037 1399 Dihedral : 3.744 23.918 1173 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.29 % Allowed : 19.87 % 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 (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: 0.78 (0.27), residues: 1061 helix: 2.30 (0.29), residues: 359 sheet: 0.27 (0.31), residues: 285 loop : -0.89 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP R 158 HIS 0.003 0.001 HIS E 35 PHE 0.026 0.001 PHE R 273 TYR 0.015 0.001 TYR E 178 ARG 0.005 0.000 ARG B 15 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 3941.59 seconds wall clock time: 67 minutes 48.79 seconds (4068.79 seconds total)