Starting phenix.real_space_refine on Fri Aug 22 23:53:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ia2_35292/08_2025/8ia2_35292.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ia2_35292/08_2025/8ia2_35292.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ia2_35292/08_2025/8ia2_35292.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ia2_35292/08_2025/8ia2_35292.map" model { file = "/net/cci-nas-00/data/ceres_data/8ia2_35292/08_2025/8ia2_35292.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ia2_35292/08_2025/8ia2_35292.cif" } resolution = 3.21 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= 0.004 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5512 2.51 5 N 1486 2.21 5 O 1601 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8653 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2237 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 14, 'TRANS': 279} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 6, 'ASP:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "D" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 489 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 19} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 1497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1497 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 44} Link IDs: {'PTRANS': 4, 'TRANS': 204} Chain breaks: 2 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 3, 'ASP:plan': 10, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 90 Chain: "C" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2435 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 6, 'ARG:plan': 6, 'ASP:plan': 8, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 110 Chain: "G" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 382 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "H" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1613 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'GLU:plan': 7, 'ASP:plan': 3, 'PHE:plan': 2, 'ARG:plan': 4, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 94 Time building chain proxies: 1.62, per 1000 atoms: 0.19 Number of scatterers: 8653 At special positions: 0 Unit cell: (83.9849, 124.383, 144.582, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1601 8.00 N 1486 7.00 C 5512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 47 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 54 " distance=2.04 Simple disulfide: pdb=" SG CYS D 34 " - pdb=" SG CYS D 55 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " 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: 0.62 Conformation dependent library (CDL) restraints added in 395.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2244 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 17 sheets defined 41.7% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 36 through 53 Processing helix chain 'A' and resid 54 through 65 Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 72 through 88 Processing helix chain 'A' and resid 88 through 98 Processing helix chain 'A' and resid 105 through 140 Proline residue: A 113 - end of helix removed outlier: 4.531A pdb=" N LEU A 117 " --> pdb=" O PRO A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.754A pdb=" N GLN A 145 " --> pdb=" O PRO A 141 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN A 146 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 174 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 198 through 230 removed outlier: 5.045A pdb=" N TRP A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Proline residue: A 214 - end of helix Processing helix chain 'A' and resid 238 through 268 removed outlier: 3.603A pdb=" N SER A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Proline residue: A 257 - end of helix Processing helix chain 'A' and resid 271 through 304 removed outlier: 4.052A pdb=" N PHE A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N SER A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LEU A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASN A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N CYS A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Proline residue: A 297 - end of helix removed outlier: 4.066A pdb=" N TYR A 300 " --> pdb=" O ASN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 314 Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 15 through 26 Processing helix chain 'D' and resid 33 through 38 Processing helix chain 'D' and resid 39 through 41 No H-bonds generated for 'chain 'D' and resid 39 through 41' Processing helix chain 'D' and resid 44 through 66 removed outlier: 4.244A pdb=" N SER D 66 " --> pdb=" O ARG D 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 31 Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.756A pdb=" N VAL B 50 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 205 removed outlier: 3.905A pdb=" N GLY B 204 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN B 205 " --> pdb=" O VAL B 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 201 through 205' Processing helix chain 'B' and resid 208 through 217 removed outlier: 4.974A pdb=" N ILE B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N HIS B 214 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU B 217 " --> pdb=" O HIS B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 255 Processing helix chain 'B' and resid 257 through 261 removed outlier: 3.600A pdb=" N ILE B 261 " --> pdb=" O LYS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 282 Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 296 through 310 Processing helix chain 'B' and resid 329 through 351 Processing helix chain 'C' and resid 4 through 26 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'G' and resid 8 through 25 removed outlier: 4.059A pdb=" N ALA G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.510A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 56 removed outlier: 3.523A pdb=" N GLY H 56 " --> pdb=" O SER H 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 53 through 56' Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 220 through 224 Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 179 Processing sheet with id=AA2, first strand: chain 'B' and resid 189 through 191 removed outlier: 6.093A pdb=" N VAL B 34 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N PHE B 200 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU B 36 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 221 " --> pdb=" O LYS B 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 225 through 227 removed outlier: 6.530A pdb=" N VAL B 226 " --> pdb=" O ASN B 270 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.755A pdb=" N LEU C 336 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS C 337 " --> pdb=" O THR C 329 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.661A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 105 removed outlier: 3.631A pdb=" N GLY C 115 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 146 through 153 removed outlier: 6.729A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.738A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.093A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.558A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AB4, first strand: chain 'H' and resid 33 through 35 removed outlier: 3.595A pdb=" N HIS H 35 " --> pdb=" O VAL H 97 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 49 through 51 Processing sheet with id=AB6, first strand: chain 'H' and resid 140 through 141 Processing sheet with id=AB7, first strand: chain 'H' and resid 146 through 148 removed outlier: 6.732A pdb=" N VAL H 147 " --> pdb=" O GLU H 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'H' and resid 194 through 195 removed outlier: 6.688A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) 449 hydrogen bonds defined for protein. 1260 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: 1.05 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2828 1.35 - 1.47: 2255 1.47 - 1.60: 3675 1.60 - 1.72: 0 1.72 - 1.84: 68 Bond restraints: 8826 Sorted by residual: bond pdb=" CA PRO C 94 " pdb=" CB PRO C 94 " ideal model delta sigma weight residual 1.533 1.489 0.045 1.42e-02 4.96e+03 9.87e+00 bond pdb=" N HIS A 194 " pdb=" CA HIS A 194 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.39e+00 bond pdb=" CA PRO G 60 " pdb=" CB PRO G 60 " ideal model delta sigma weight residual 1.534 1.496 0.038 1.49e-02 4.50e+03 6.50e+00 bond pdb=" N PHE A 172 " pdb=" CA PHE A 172 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.31e-02 5.83e+03 6.33e+00 bond pdb=" N ILE C 93 " pdb=" CA ILE C 93 " ideal model delta sigma weight residual 1.460 1.476 -0.017 7.50e-03 1.78e+04 5.05e+00 ... (remaining 8821 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 11425 1.54 - 3.08: 490 3.08 - 4.62: 106 4.62 - 6.16: 16 6.16 - 7.70: 3 Bond angle restraints: 12040 Sorted by residual: angle pdb=" N PRO H 181 " pdb=" CA PRO H 181 " pdb=" CB PRO H 181 " ideal model delta sigma weight residual 103.31 109.24 -5.93 8.90e-01 1.26e+00 4.44e+01 angle pdb=" N ARG A 198 " pdb=" CA ARG A 198 " pdb=" C ARG A 198 " ideal model delta sigma weight residual 114.56 108.75 5.81 1.27e+00 6.20e-01 2.09e+01 angle pdb=" CA PHE A 172 " pdb=" CB PHE A 172 " pdb=" CG PHE A 172 " ideal model delta sigma weight residual 113.80 118.28 -4.48 1.00e+00 1.00e+00 2.01e+01 angle pdb=" N PRO G 60 " pdb=" CA PRO G 60 " pdb=" CB PRO G 60 " ideal model delta sigma weight residual 103.51 107.75 -4.24 9.60e-01 1.09e+00 1.95e+01 angle pdb=" O ILE C 93 " pdb=" C ILE C 93 " pdb=" N PRO C 94 " ideal model delta sigma weight residual 121.57 125.21 -3.64 8.70e-01 1.32e+00 1.75e+01 ... (remaining 12035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 4769 17.99 - 35.97: 326 35.97 - 53.96: 57 53.96 - 71.95: 5 71.95 - 89.94: 8 Dihedral angle restraints: 5165 sinusoidal: 1692 harmonic: 3473 Sorted by residual: dihedral pdb=" CA GLN A 145 " pdb=" C GLN A 145 " pdb=" N ASN A 146 " pdb=" CA ASN A 146 " ideal model delta harmonic sigma weight residual 180.00 154.61 25.39 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA TRP C 82 " pdb=" C TRP C 82 " pdb=" N ASP C 83 " pdb=" CA ASP C 83 " ideal model delta harmonic sigma weight residual 180.00 154.91 25.09 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CB CYS D 34 " pdb=" SG CYS D 34 " pdb=" SG CYS D 55 " pdb=" CB CYS D 55 " ideal model delta sinusoidal sigma weight residual -86.00 -126.01 40.01 1 1.00e+01 1.00e-02 2.25e+01 ... (remaining 5162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1005 0.041 - 0.082: 320 0.082 - 0.123: 83 0.123 - 0.164: 22 0.164 - 0.205: 1 Chirality restraints: 1431 Sorted by residual: chirality pdb=" CA PRO H 181 " pdb=" N PRO H 181 " pdb=" C PRO H 181 " pdb=" CB PRO H 181 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ILE C 93 " pdb=" N ILE C 93 " pdb=" C ILE C 93 " pdb=" CB ILE C 93 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.71e-01 chirality pdb=" CA ILE C 232 " pdb=" N ILE C 232 " pdb=" C ILE C 232 " pdb=" CB ILE C 232 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.61e-01 ... (remaining 1428 not shown) Planarity restraints: 1536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN G 59 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.14e+00 pdb=" C ASN G 59 " 0.039 2.00e-02 2.50e+03 pdb=" O ASN G 59 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO G 60 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER H 106 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO H 107 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO H 107 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 107 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 183 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.45e+00 pdb=" N PRO A 184 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 184 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 184 " 0.026 5.00e-02 4.00e+02 ... (remaining 1533 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 362 2.71 - 3.26: 9595 3.26 - 3.81: 13902 3.81 - 4.35: 17463 4.35 - 4.90: 29824 Nonbonded interactions: 71146 Sorted by model distance: nonbonded pdb=" N GLU H 220 " pdb=" OE1 GLU H 220 " model vdw 2.166 3.120 nonbonded pdb=" O GLN B 333 " pdb=" NE2 GLN B 333 " model vdw 2.202 3.120 nonbonded pdb=" N GLN D 3 " pdb=" OE1 GLN D 3 " model vdw 2.207 3.120 nonbonded pdb=" O VAL A 58 " pdb=" OG1 THR A 62 " model vdw 2.211 3.040 nonbonded pdb=" O SER A 237 " pdb=" OG1 THR A 238 " model vdw 2.213 3.040 ... (remaining 71141 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: 3.900 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: 0.010 Process input model: 7.390 Find NCS groups from input model: 0.050 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8832 Z= 0.222 Angle : 0.763 7.695 12052 Z= 0.445 Chirality : 0.044 0.205 1431 Planarity : 0.005 0.050 1536 Dihedral : 13.187 89.935 2903 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 0.49 % Allowed : 9.59 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.13 (0.23), residues: 1183 helix: -0.05 (0.24), residues: 410 sheet: -1.02 (0.29), residues: 284 loop : -1.02 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 48 TYR 0.021 0.003 TYR A 181 PHE 0.027 0.002 PHE B 192 TRP 0.022 0.003 TRP C 82 HIS 0.009 0.002 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 8826) covalent geometry : angle 0.76075 (12040) SS BOND : bond 0.00533 ( 6) SS BOND : angle 2.14569 ( 12) hydrogen bonds : bond 0.15907 ( 449) hydrogen bonds : angle 7.53949 ( 1260) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 142 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.7672 (mm) cc_final: 0.7462 (mp) REVERT: A 195 ASP cc_start: 0.7413 (t0) cc_final: 0.7207 (t0) REVERT: A 282 ASP cc_start: 0.6941 (t70) cc_final: 0.6686 (t0) REVERT: B 208 GLU cc_start: 0.8070 (tt0) cc_final: 0.7810 (tt0) REVERT: B 309 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7055 (mt-10) REVERT: C 247 ASP cc_start: 0.7502 (t0) cc_final: 0.7282 (t0) REVERT: G 42 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7239 (mm-30) REVERT: H 6 GLU cc_start: 0.3203 (mt-10) cc_final: 0.2679 (mt-10) REVERT: H 55 SER cc_start: 0.7763 (m) cc_final: 0.7388 (p) outliers start: 4 outliers final: 3 residues processed: 144 average time/residue: 0.0822 time to fit residues: 15.9769 Evaluate side-chains 129 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain H residue 31 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.135158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.114005 restraints weight = 17704.680| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.51 r_work: 0.3661 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8832 Z= 0.201 Angle : 0.711 8.991 12052 Z= 0.371 Chirality : 0.046 0.156 1431 Planarity : 0.005 0.050 1536 Dihedral : 6.365 64.371 1279 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.94 % Allowed : 12.14 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.74 (0.24), residues: 1183 helix: 0.43 (0.24), residues: 421 sheet: -1.05 (0.28), residues: 284 loop : -0.80 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 87 TYR 0.020 0.002 TYR A 181 PHE 0.021 0.002 PHE H 212 TRP 0.025 0.003 TRP C 82 HIS 0.008 0.002 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 8826) covalent geometry : angle 0.70868 (12040) SS BOND : bond 0.00659 ( 6) SS BOND : angle 2.01902 ( 12) hydrogen bonds : bond 0.04513 ( 449) hydrogen bonds : angle 5.85251 ( 1260) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.343 Fit side-chains REVERT: A 282 ASP cc_start: 0.6883 (t70) cc_final: 0.6355 (t0) REVERT: A 290 TYR cc_start: 0.8229 (m-80) cc_final: 0.7895 (m-80) REVERT: G 42 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7356 (mm-30) REVERT: H 50 TYR cc_start: 0.7657 (OUTLIER) cc_final: 0.6611 (t80) REVERT: H 55 SER cc_start: 0.7755 (m) cc_final: 0.7377 (p) REVERT: H 220 GLU cc_start: 0.7272 (mp0) cc_final: 0.6878 (mm-30) outliers start: 16 outliers final: 11 residues processed: 143 average time/residue: 0.1051 time to fit residues: 20.6953 Evaluate side-chains 134 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 144 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 106 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 0.0980 chunk 100 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.137665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.116829 restraints weight = 17381.643| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.49 r_work: 0.3744 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8832 Z= 0.156 Angle : 0.636 8.527 12052 Z= 0.331 Chirality : 0.044 0.159 1431 Planarity : 0.005 0.058 1536 Dihedral : 5.846 65.137 1278 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.03 % Allowed : 14.44 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.54 (0.25), residues: 1183 helix: 0.76 (0.25), residues: 421 sheet: -1.18 (0.28), residues: 288 loop : -0.68 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 304 TYR 0.014 0.002 TYR A 181 PHE 0.014 0.002 PHE A 93 TRP 0.018 0.002 TRP C 82 HIS 0.006 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 8826) covalent geometry : angle 0.63313 (12040) SS BOND : bond 0.00660 ( 6) SS BOND : angle 2.04501 ( 12) hydrogen bonds : bond 0.03934 ( 449) hydrogen bonds : angle 5.50550 ( 1260) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 94 THR cc_start: 0.6872 (p) cc_final: 0.6626 (p) REVERT: A 282 ASP cc_start: 0.7005 (t70) cc_final: 0.6727 (t0) REVERT: A 290 TYR cc_start: 0.8187 (m-80) cc_final: 0.7822 (m-80) REVERT: D 74 ARG cc_start: 0.5887 (OUTLIER) cc_final: 0.5095 (mtt90) REVERT: C 81 ILE cc_start: 0.7144 (OUTLIER) cc_final: 0.6920 (pt) REVERT: C 304 ARG cc_start: 0.5430 (mmp-170) cc_final: 0.4486 (mmp-170) REVERT: G 42 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7427 (mm-30) REVERT: H 55 SER cc_start: 0.7762 (m) cc_final: 0.7359 (p) outliers start: 25 outliers final: 15 residues processed: 146 average time/residue: 0.1039 time to fit residues: 20.7657 Evaluate side-chains 137 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 189 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 90 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN B 330 ASN C 119 ASN H 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.137934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.116292 restraints weight = 17431.835| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.59 r_work: 0.3652 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8832 Z= 0.173 Angle : 0.641 8.571 12052 Z= 0.333 Chirality : 0.044 0.157 1431 Planarity : 0.004 0.059 1536 Dihedral : 5.661 65.112 1278 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 5.10 % Allowed : 14.32 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.49 (0.25), residues: 1183 helix: 0.88 (0.25), residues: 421 sheet: -1.20 (0.29), residues: 276 loop : -0.74 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 304 TYR 0.016 0.002 TYR A 258 PHE 0.024 0.002 PHE H 212 TRP 0.016 0.002 TRP C 82 HIS 0.005 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 8826) covalent geometry : angle 0.63808 (12040) SS BOND : bond 0.00623 ( 6) SS BOND : angle 2.04703 ( 12) hydrogen bonds : bond 0.03933 ( 449) hydrogen bonds : angle 5.43175 ( 1260) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 94 THR cc_start: 0.6861 (p) cc_final: 0.6592 (p) REVERT: A 282 ASP cc_start: 0.6809 (t70) cc_final: 0.6496 (t0) REVERT: A 290 TYR cc_start: 0.8225 (m-80) cc_final: 0.7922 (m-80) REVERT: D 74 ARG cc_start: 0.6092 (OUTLIER) cc_final: 0.5199 (mtt90) REVERT: B 309 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7410 (mt-10) REVERT: C 81 ILE cc_start: 0.7294 (OUTLIER) cc_final: 0.7080 (pt) REVERT: C 211 TRP cc_start: 0.6492 (OUTLIER) cc_final: 0.5600 (m-10) REVERT: G 42 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7376 (mm-30) REVERT: H 50 TYR cc_start: 0.7649 (OUTLIER) cc_final: 0.6443 (t80) REVERT: H 55 SER cc_start: 0.7798 (OUTLIER) cc_final: 0.7385 (p) REVERT: H 192 MET cc_start: 0.6567 (tpp) cc_final: 0.6314 (tpp) outliers start: 42 outliers final: 27 residues processed: 156 average time/residue: 0.0981 time to fit residues: 21.1756 Evaluate side-chains 154 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 189 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 83 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 0.0370 chunk 48 optimal weight: 0.3980 chunk 77 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.135847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.114862 restraints weight = 17730.821| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.52 r_work: 0.3731 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8832 Z= 0.153 Angle : 0.626 8.421 12052 Z= 0.324 Chirality : 0.043 0.138 1431 Planarity : 0.004 0.061 1536 Dihedral : 5.500 65.999 1278 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 4.13 % Allowed : 15.78 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.42 (0.25), residues: 1183 helix: 0.97 (0.25), residues: 422 sheet: -1.24 (0.28), residues: 291 loop : -0.62 (0.31), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 304 TYR 0.015 0.002 TYR A 258 PHE 0.026 0.002 PHE H 212 TRP 0.016 0.002 TRP C 82 HIS 0.004 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 8826) covalent geometry : angle 0.62341 (12040) SS BOND : bond 0.00612 ( 6) SS BOND : angle 2.05476 ( 12) hydrogen bonds : bond 0.03744 ( 449) hydrogen bonds : angle 5.34004 ( 1260) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 THR cc_start: 0.6904 (p) cc_final: 0.6629 (p) REVERT: A 282 ASP cc_start: 0.6980 (t70) cc_final: 0.6675 (t0) REVERT: A 290 TYR cc_start: 0.8198 (m-80) cc_final: 0.7826 (m-80) REVERT: D 74 ARG cc_start: 0.5993 (OUTLIER) cc_final: 0.5157 (mtt90) REVERT: B 309 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7404 (mt-10) REVERT: C 81 ILE cc_start: 0.7216 (OUTLIER) cc_final: 0.6997 (pt) REVERT: C 211 TRP cc_start: 0.6457 (OUTLIER) cc_final: 0.5615 (m-10) REVERT: G 42 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7375 (mm-30) REVERT: H 55 SER cc_start: 0.7866 (OUTLIER) cc_final: 0.7464 (p) REVERT: H 192 MET cc_start: 0.6608 (tpp) cc_final: 0.6325 (tpp) outliers start: 34 outliers final: 28 residues processed: 148 average time/residue: 0.1002 time to fit residues: 20.5923 Evaluate side-chains 151 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 189 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 34 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 99 optimal weight: 0.2980 chunk 77 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN D 71 GLN C 183 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.135341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.114510 restraints weight = 17638.698| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.48 r_work: 0.3660 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8832 Z= 0.168 Angle : 0.639 8.264 12052 Z= 0.329 Chirality : 0.043 0.156 1431 Planarity : 0.004 0.061 1536 Dihedral : 5.464 65.890 1278 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 4.85 % Allowed : 16.38 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.45 (0.25), residues: 1183 helix: 0.98 (0.25), residues: 420 sheet: -1.31 (0.28), residues: 291 loop : -0.64 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 304 TYR 0.017 0.002 TYR A 258 PHE 0.026 0.002 PHE H 212 TRP 0.015 0.002 TRP C 82 HIS 0.004 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 8826) covalent geometry : angle 0.63581 (12040) SS BOND : bond 0.00560 ( 6) SS BOND : angle 2.07091 ( 12) hydrogen bonds : bond 0.03817 ( 449) hydrogen bonds : angle 5.33198 ( 1260) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 124 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 THR cc_start: 0.6922 (p) cc_final: 0.6635 (p) REVERT: A 290 TYR cc_start: 0.8273 (m-80) cc_final: 0.7970 (m-80) REVERT: D 71 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8221 (tm-30) REVERT: D 74 ARG cc_start: 0.6113 (OUTLIER) cc_final: 0.5256 (mtt90) REVERT: B 309 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7285 (mt-10) REVERT: C 81 ILE cc_start: 0.7287 (OUTLIER) cc_final: 0.7068 (pt) REVERT: C 211 TRP cc_start: 0.6437 (OUTLIER) cc_final: 0.5638 (m-10) REVERT: G 42 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7329 (mm-30) REVERT: H 50 TYR cc_start: 0.7623 (OUTLIER) cc_final: 0.6423 (t80) REVERT: H 55 SER cc_start: 0.7821 (OUTLIER) cc_final: 0.7409 (p) REVERT: H 192 MET cc_start: 0.6648 (tpp) cc_final: 0.6373 (tpp) outliers start: 40 outliers final: 31 residues processed: 156 average time/residue: 0.0922 time to fit residues: 20.2208 Evaluate side-chains 156 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain D residue 71 GLN Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 189 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.136110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.114728 restraints weight = 17656.811| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.60 r_work: 0.3640 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8832 Z= 0.187 Angle : 0.657 8.045 12052 Z= 0.337 Chirality : 0.044 0.155 1431 Planarity : 0.004 0.061 1536 Dihedral : 5.412 65.992 1275 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 5.58 % Allowed : 16.14 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1183 helix: 0.92 (0.25), residues: 420 sheet: -1.33 (0.28), residues: 291 loop : -0.66 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 304 TYR 0.019 0.002 TYR A 258 PHE 0.032 0.002 PHE H 212 TRP 0.014 0.002 TRP C 82 HIS 0.005 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 8826) covalent geometry : angle 0.65370 (12040) SS BOND : bond 0.00598 ( 6) SS BOND : angle 2.09504 ( 12) hydrogen bonds : bond 0.03869 ( 449) hydrogen bonds : angle 5.38904 ( 1260) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 118 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 THR cc_start: 0.7001 (p) cc_final: 0.6736 (p) REVERT: A 282 ASP cc_start: 0.6692 (t0) cc_final: 0.6329 (t0) REVERT: A 290 TYR cc_start: 0.8256 (m-80) cc_final: 0.7935 (m-80) REVERT: B 309 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7381 (mt-10) REVERT: C 211 TRP cc_start: 0.6495 (OUTLIER) cc_final: 0.5724 (m-10) REVERT: G 42 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7368 (mm-30) REVERT: H 50 TYR cc_start: 0.7669 (OUTLIER) cc_final: 0.6461 (t80) REVERT: H 55 SER cc_start: 0.7833 (OUTLIER) cc_final: 0.7417 (p) REVERT: H 173 TYR cc_start: 0.7779 (m-80) cc_final: 0.7521 (m-80) REVERT: H 192 MET cc_start: 0.6734 (tpp) cc_final: 0.6452 (tpp) outliers start: 46 outliers final: 35 residues processed: 154 average time/residue: 0.0872 time to fit residues: 19.2649 Evaluate side-chains 154 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 116 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 189 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 23 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 44 optimal weight: 0.0670 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 52 optimal weight: 0.0030 chunk 55 optimal weight: 0.7980 chunk 4 optimal weight: 0.0570 overall best weight: 0.3446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.139013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.118062 restraints weight = 17454.242| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.53 r_work: 0.3757 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8832 Z= 0.125 Angle : 0.608 8.047 12052 Z= 0.312 Chirality : 0.042 0.169 1431 Planarity : 0.004 0.063 1536 Dihedral : 5.131 67.498 1275 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.00 % Allowed : 18.08 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.25 (0.25), residues: 1183 helix: 1.19 (0.26), residues: 419 sheet: -1.10 (0.31), residues: 255 loop : -0.72 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 304 TYR 0.013 0.001 TYR H 190 PHE 0.031 0.001 PHE H 212 TRP 0.015 0.001 TRP C 82 HIS 0.005 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8826) covalent geometry : angle 0.60444 (12040) SS BOND : bond 0.00609 ( 6) SS BOND : angle 2.05605 ( 12) hydrogen bonds : bond 0.03481 ( 449) hydrogen bonds : angle 5.16519 ( 1260) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 ASP cc_start: 0.6661 (t0) cc_final: 0.6334 (t0) REVERT: D 28 VAL cc_start: 0.6645 (m) cc_final: 0.6388 (m) REVERT: B 309 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7377 (mt-10) REVERT: G 42 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7383 (mm-30) REVERT: H 173 TYR cc_start: 0.7735 (m-80) cc_final: 0.7457 (m-80) REVERT: H 192 MET cc_start: 0.6682 (tpp) cc_final: 0.6441 (tpp) outliers start: 33 outliers final: 28 residues processed: 147 average time/residue: 0.0923 time to fit residues: 19.1158 Evaluate side-chains 146 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 189 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 86 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 111 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.138354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.117045 restraints weight = 17443.311| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.56 r_work: 0.3731 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8832 Z= 0.148 Angle : 0.635 9.086 12052 Z= 0.323 Chirality : 0.043 0.152 1431 Planarity : 0.004 0.062 1536 Dihedral : 5.153 66.997 1275 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.64 % Allowed : 18.81 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.33 (0.25), residues: 1183 helix: 1.10 (0.26), residues: 420 sheet: -1.20 (0.29), residues: 277 loop : -0.66 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 304 TYR 0.016 0.002 TYR C 105 PHE 0.016 0.001 PHE H 212 TRP 0.015 0.001 TRP C 82 HIS 0.004 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8826) covalent geometry : angle 0.63154 (12040) SS BOND : bond 0.00543 ( 6) SS BOND : angle 2.10633 ( 12) hydrogen bonds : bond 0.03626 ( 449) hydrogen bonds : angle 5.19443 ( 1260) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 28 VAL cc_start: 0.6595 (m) cc_final: 0.6326 (m) REVERT: B 309 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7399 (mt-10) REVERT: G 42 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7407 (mm-30) REVERT: H 192 MET cc_start: 0.6730 (tpp) cc_final: 0.6472 (tpp) outliers start: 30 outliers final: 29 residues processed: 140 average time/residue: 0.0895 time to fit residues: 17.9565 Evaluate side-chains 144 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 189 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 48 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 100 optimal weight: 0.0270 chunk 98 optimal weight: 0.2980 chunk 81 optimal weight: 0.7980 chunk 63 optimal weight: 0.0970 chunk 59 optimal weight: 9.9990 chunk 104 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.140365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.119111 restraints weight = 17429.988| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.62 r_work: 0.3750 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8832 Z= 0.125 Angle : 0.614 11.418 12052 Z= 0.312 Chirality : 0.042 0.154 1431 Planarity : 0.004 0.063 1536 Dihedral : 5.008 66.951 1275 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.88 % Allowed : 18.81 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.20 (0.25), residues: 1183 helix: 1.20 (0.26), residues: 420 sheet: -1.03 (0.30), residues: 269 loop : -0.66 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 304 TYR 0.013 0.001 TYR A 258 PHE 0.020 0.001 PHE H 212 TRP 0.018 0.001 TRP C 82 HIS 0.003 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8826) covalent geometry : angle 0.61123 (12040) SS BOND : bond 0.00568 ( 6) SS BOND : angle 2.07757 ( 12) hydrogen bonds : bond 0.03431 ( 449) hydrogen bonds : angle 5.06280 ( 1260) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 290 TYR cc_start: 0.8202 (m-80) cc_final: 0.7777 (m-80) REVERT: D 28 VAL cc_start: 0.6390 (m) cc_final: 0.5987 (m) REVERT: D 74 ARG cc_start: 0.5680 (OUTLIER) cc_final: 0.4942 (mtt90) REVERT: B 309 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7353 (mt-10) REVERT: G 42 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7315 (mm-30) REVERT: H 55 SER cc_start: 0.7889 (m) cc_final: 0.7488 (p) REVERT: H 173 TYR cc_start: 0.7764 (m-80) cc_final: 0.7417 (m-80) REVERT: H 192 MET cc_start: 0.6706 (tpp) cc_final: 0.6446 (tpp) outliers start: 32 outliers final: 28 residues processed: 144 average time/residue: 0.0919 time to fit residues: 18.9034 Evaluate side-chains 144 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 189 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 71 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.139533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.118331 restraints weight = 17519.382| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.58 r_work: 0.3755 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 8832 Z= 0.194 Angle : 0.938 59.192 12052 Z= 0.528 Chirality : 0.047 0.733 1431 Planarity : 0.004 0.063 1536 Dihedral : 5.050 66.836 1275 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.00 % Allowed : 18.33 % Favored : 77.67 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % 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: -0.22 (0.25), residues: 1183 helix: 1.18 (0.26), residues: 420 sheet: -1.02 (0.30), residues: 269 loop : -0.68 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 74 TYR 0.014 0.002 TYR A 258 PHE 0.017 0.001 PHE H 212 TRP 0.017 0.001 TRP C 82 HIS 0.004 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 8826) covalent geometry : angle 0.93652 (12040) SS BOND : bond 0.00521 ( 6) SS BOND : angle 2.05707 ( 12) hydrogen bonds : bond 0.03482 ( 449) hydrogen bonds : angle 5.06093 ( 1260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2278.02 seconds wall clock time: 39 minutes 56.84 seconds (2396.84 seconds total)