Starting phenix.real_space_refine on Tue Apr 29 12:10:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ia2_35292/04_2025/8ia2_35292.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ia2_35292/04_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_35292/04_2025/8ia2_35292.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ia2_35292/04_2025/8ia2_35292.map" model { file = "/net/cci-nas-00/data/ceres_data/8ia2_35292/04_2025/8ia2_35292.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ia2_35292/04_2025/8ia2_35292.cif" } resolution = 3.21 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= 0.004 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'ARG:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'ASP: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: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 1} 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: {'GLN:plan1': 1, 'ASP:plan': 10, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} 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: {'GLN:plan1': 6, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 5, 'ARG:plan': 6} 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: {'GLU:plan': 3, 'ARG:plan': 2} 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, 'HIS:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 94 Time building chain proxies: 6.13, per 1000 atoms: 0.71 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: 2.43 Conformation dependent library (CDL) restraints added in 1.1 seconds 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 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: 1.15 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: 2.47 Time building geometry restraints manager: 2.82 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: 2.930 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.330 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.930 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.23), 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 TRP 0.022 0.003 TRP C 82 HIS 0.009 0.002 HIS A 100 PHE 0.027 0.002 PHE B 192 TYR 0.021 0.003 TYR A 181 ARG 0.004 0.001 ARG C 48 Details of bonding type rmsd hydrogen bonds : bond 0.15907 ( 449) hydrogen bonds : angle 7.53949 ( 1260) SS BOND : bond 0.00533 ( 6) SS BOND : angle 2.14569 ( 12) covalent geometry : bond 0.00459 ( 8826) covalent geometry : angle 0.76075 (12040) *********************** 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 : 0.896 Fit side-chains 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: 0.7813 (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: 0.7240 (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: 0.2189 time to fit residues: 42.8699 Evaluate side-chains 128 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 125 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 106 optimal weight: 0.0670 overall best weight: 0.6920 ------------------------------------------------------------------------------- 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 = 0.4170 r_free = 0.4170 target = 0.134720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.114354 restraints weight = 17672.161| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.44 r_work: 0.3739 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8832 Z= 0.175 Angle : 0.687 8.734 12052 Z= 0.359 Chirality : 0.045 0.155 1431 Planarity : 0.005 0.051 1536 Dihedral : 6.221 64.276 1279 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.94 % Allowed : 11.77 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.67 (0.24), residues: 1183 helix: 0.53 (0.25), residues: 421 sheet: -1.05 (0.29), residues: 277 loop : -0.79 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 82 HIS 0.007 0.001 HIS A 100 PHE 0.021 0.002 PHE H 212 TYR 0.019 0.002 TYR A 181 ARG 0.003 0.001 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.04375 ( 449) hydrogen bonds : angle 5.77532 ( 1260) SS BOND : bond 0.00607 ( 6) SS BOND : angle 2.00415 ( 12) covalent geometry : bond 0.00405 ( 8826) covalent geometry : angle 0.68441 (12040) *********************** 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 146 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.894 Fit side-chains REVERT: A 282 ASP cc_start: 0.6847 (t70) cc_final: 0.6333 (t0) REVERT: A 290 TYR cc_start: 0.8147 (m-80) cc_final: 0.7741 (m-80) REVERT: C 234 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8566 (m-80) REVERT: G 42 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7365 (mm-30) REVERT: H 50 TYR cc_start: 0.7582 (OUTLIER) cc_final: 0.6572 (t80) REVERT: H 55 SER cc_start: 0.7749 (m) cc_final: 0.7407 (p) REVERT: H 220 GLU cc_start: 0.7280 (mp0) cc_final: 0.6862 (mm-30) outliers start: 16 outliers final: 11 residues processed: 141 average time/residue: 0.2150 time to fit residues: 41.6767 Evaluate side-chains 134 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 234 PHE 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 48 optimal weight: 0.4980 chunk 62 optimal weight: 0.5980 chunk 58 optimal weight: 7.9990 chunk 75 optimal weight: 0.2980 chunk 27 optimal weight: 0.0970 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.137867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.116968 restraints weight = 17632.405| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.51 r_work: 0.3751 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8832 Z= 0.143 Angle : 0.619 8.398 12052 Z= 0.323 Chirality : 0.043 0.153 1431 Planarity : 0.004 0.058 1536 Dihedral : 5.751 67.728 1278 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.28 % Allowed : 13.59 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.43 (0.25), residues: 1183 helix: 0.87 (0.25), residues: 421 sheet: -1.13 (0.28), residues: 288 loop : -0.64 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 82 HIS 0.005 0.001 HIS A 100 PHE 0.013 0.001 PHE A 93 TYR 0.014 0.002 TYR A 181 ARG 0.004 0.000 ARG C 304 Details of bonding type rmsd hydrogen bonds : bond 0.03822 ( 449) hydrogen bonds : angle 5.39982 ( 1260) SS BOND : bond 0.00565 ( 6) SS BOND : angle 2.06801 ( 12) covalent geometry : bond 0.00326 ( 8826) covalent geometry : angle 0.61622 (12040) *********************** 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 154 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: A 94 THR cc_start: 0.7091 (p) cc_final: 0.6840 (p) REVERT: A 282 ASP cc_start: 0.7061 (t70) cc_final: 0.6764 (t0) REVERT: A 290 TYR cc_start: 0.8140 (m-80) cc_final: 0.7761 (m-80) REVERT: D 74 ARG cc_start: 0.6074 (OUTLIER) cc_final: 0.5312 (mtt90) REVERT: C 81 ILE cc_start: 0.7265 (OUTLIER) cc_final: 0.7017 (pt) REVERT: C 270 ILE cc_start: 0.8709 (pt) cc_final: 0.8324 (mm) REVERT: C 304 ARG cc_start: 0.5469 (mmp-170) cc_final: 0.4735 (mmp-170) REVERT: G 42 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7383 (mm-30) REVERT: H 55 SER cc_start: 0.7941 (m) cc_final: 0.7541 (p) outliers start: 27 outliers final: 17 residues processed: 146 average time/residue: 0.2070 time to fit residues: 41.4919 Evaluate side-chains 137 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 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 232 ILE 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 116 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 210 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 94 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 44 optimal weight: 0.0010 chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN B 245 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.138600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.117044 restraints weight = 17220.385| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.57 r_work: 0.3728 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8832 Z= 0.148 Angle : 0.619 8.461 12052 Z= 0.320 Chirality : 0.043 0.152 1431 Planarity : 0.004 0.059 1536 Dihedral : 5.581 64.930 1278 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.88 % Allowed : 15.05 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.25), residues: 1183 helix: 0.99 (0.25), residues: 422 sheet: -1.08 (0.29), residues: 276 loop : -0.66 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 82 HIS 0.004 0.001 HIS C 91 PHE 0.027 0.002 PHE H 212 TYR 0.014 0.002 TYR A 258 ARG 0.004 0.000 ARG C 304 Details of bonding type rmsd hydrogen bonds : bond 0.03738 ( 449) hydrogen bonds : angle 5.30367 ( 1260) SS BOND : bond 0.00543 ( 6) SS BOND : angle 2.03559 ( 12) covalent geometry : bond 0.00342 ( 8826) covalent geometry : angle 0.61555 (12040) *********************** 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 153 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: A 94 THR cc_start: 0.6928 (p) cc_final: 0.6661 (p) REVERT: A 282 ASP cc_start: 0.7028 (t70) cc_final: 0.6732 (t0) REVERT: A 290 TYR cc_start: 0.8164 (m-80) cc_final: 0.7852 (m-80) REVERT: D 74 ARG cc_start: 0.5873 (OUTLIER) cc_final: 0.5090 (mtt90) REVERT: B 309 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7444 (mt-10) REVERT: C 81 ILE cc_start: 0.7200 (OUTLIER) cc_final: 0.6969 (pt) REVERT: G 42 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7351 (mm-30) REVERT: H 55 SER cc_start: 0.7727 (m) cc_final: 0.7313 (p) REVERT: H 192 MET cc_start: 0.6542 (tpp) cc_final: 0.6290 (tpp) outliers start: 32 outliers final: 24 residues processed: 144 average time/residue: 0.2047 time to fit residues: 41.8671 Evaluate side-chains 145 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 1.197 ------------------------------------------------------------------------------- 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 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 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 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 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 3 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 0.5980 chunk 70 optimal weight: 0.0570 chunk 101 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.138762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.117251 restraints weight = 17109.466| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.57 r_work: 0.3660 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.2353 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= 0.163 Angle : 0.627 8.318 12052 Z= 0.325 Chirality : 0.043 0.154 1431 Planarity : 0.004 0.061 1536 Dihedral : 5.506 65.868 1278 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 4.85 % Allowed : 15.29 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.25), residues: 1183 helix: 0.99 (0.25), residues: 422 sheet: -1.15 (0.29), residues: 278 loop : -0.66 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 82 HIS 0.004 0.001 HIS A 100 PHE 0.026 0.002 PHE H 212 TYR 0.016 0.002 TYR A 258 ARG 0.004 0.000 ARG C 304 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 449) hydrogen bonds : angle 5.31558 ( 1260) SS BOND : bond 0.00675 ( 6) SS BOND : angle 2.02804 ( 12) covalent geometry : bond 0.00381 ( 8826) covalent geometry : angle 0.62448 (12040) *********************** 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 163 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 THR cc_start: 0.6964 (p) cc_final: 0.6687 (p) REVERT: A 282 ASP cc_start: 0.7003 (t70) cc_final: 0.6709 (t0) REVERT: D 74 ARG cc_start: 0.6008 (OUTLIER) cc_final: 0.5155 (mtt90) REVERT: C 81 ILE cc_start: 0.7283 (OUTLIER) cc_final: 0.7049 (pt) REVERT: G 42 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7360 (mm-30) REVERT: H 50 TYR cc_start: 0.7669 (OUTLIER) cc_final: 0.6264 (t80) REVERT: H 55 SER cc_start: 0.7762 (OUTLIER) cc_final: 0.7341 (p) REVERT: H 192 MET cc_start: 0.6611 (tpp) cc_final: 0.6315 (tpp) outliers start: 40 outliers final: 31 residues processed: 152 average time/residue: 0.2803 time to fit residues: 58.8004 Evaluate side-chains 152 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 19 optimal weight: 0.6980 chunk 112 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 GLN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.136411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.114952 restraints weight = 17165.482| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.55 r_work: 0.3652 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.2486 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= 0.177 Angle : 0.641 8.152 12052 Z= 0.331 Chirality : 0.043 0.154 1431 Planarity : 0.004 0.061 1536 Dihedral : 5.476 65.924 1278 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 4.73 % Allowed : 16.87 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1183 helix: 0.95 (0.25), residues: 420 sheet: -1.25 (0.29), residues: 285 loop : -0.64 (0.31), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 82 HIS 0.005 0.001 HIS C 91 PHE 0.028 0.002 PHE H 212 TYR 0.018 0.002 TYR A 258 ARG 0.003 0.000 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 449) hydrogen bonds : angle 5.35994 ( 1260) SS BOND : bond 0.00582 ( 6) SS BOND : angle 2.06107 ( 12) covalent geometry : bond 0.00417 ( 8826) covalent geometry : angle 0.63825 (12040) *********************** 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 158 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 THR cc_start: 0.7039 (p) cc_final: 0.6757 (p) REVERT: A 290 TYR cc_start: 0.8240 (m-80) cc_final: 0.7936 (m-80) REVERT: D 71 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8210 (tm-30) REVERT: D 74 ARG cc_start: 0.6155 (OUTLIER) cc_final: 0.5280 (mtt90) REVERT: C 211 TRP cc_start: 0.6493 (OUTLIER) cc_final: 0.5721 (m-10) REVERT: G 42 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7347 (mm-30) REVERT: H 50 TYR cc_start: 0.7662 (OUTLIER) cc_final: 0.6344 (t80) REVERT: H 55 SER cc_start: 0.7796 (m) cc_final: 0.7376 (p) REVERT: H 192 MET cc_start: 0.6706 (tpp) cc_final: 0.6417 (tpp) outliers start: 39 outliers final: 29 residues processed: 152 average time/residue: 0.2017 time to fit residues: 43.0102 Evaluate side-chains 145 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 189 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 89 optimal weight: 10.0000 chunk 110 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 32 optimal weight: 0.0000 chunk 27 optimal weight: 0.4980 chunk 105 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 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 = 0.4179 r_free = 0.4179 target = 0.137105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.115920 restraints weight = 17610.662| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.53 r_work: 0.3675 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8832 Z= 0.147 Angle : 0.626 7.976 12052 Z= 0.321 Chirality : 0.043 0.159 1431 Planarity : 0.004 0.062 1536 Dihedral : 5.240 64.883 1275 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.37 % Allowed : 17.84 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.25), residues: 1183 helix: 1.04 (0.25), residues: 418 sheet: -1.25 (0.29), residues: 285 loop : -0.65 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.006 0.001 HIS C 91 PHE 0.035 0.002 PHE H 212 TYR 0.017 0.002 TYR C 105 ARG 0.006 0.000 ARG C 304 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 449) hydrogen bonds : angle 5.24373 ( 1260) SS BOND : bond 0.00574 ( 6) SS BOND : angle 2.04088 ( 12) covalent geometry : bond 0.00343 ( 8826) covalent geometry : angle 0.62280 (12040) *********************** 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 156 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 THR cc_start: 0.6970 (p) cc_final: 0.6697 (p) REVERT: A 282 ASP cc_start: 0.6877 (t0) cc_final: 0.6507 (t0) REVERT: B 309 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7156 (mt-10) REVERT: C 211 TRP cc_start: 0.6416 (OUTLIER) cc_final: 0.5623 (m-10) REVERT: G 42 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7355 (mm-30) REVERT: H 55 SER cc_start: 0.7766 (m) cc_final: 0.7357 (p) REVERT: H 192 MET cc_start: 0.6656 (tpp) cc_final: 0.6379 (tpp) outliers start: 36 outliers final: 34 residues processed: 146 average time/residue: 0.1979 time to fit residues: 40.5004 Evaluate side-chains 151 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 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 7 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 90 VAL 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 263 THR Chi-restraints excluded: chain C residue 266 HIS 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 41 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 0.0170 chunk 5 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 21 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 89 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.137405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.116285 restraints weight = 17724.686| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.52 r_work: 0.3718 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2714 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= 0.142 Angle : 0.622 7.985 12052 Z= 0.318 Chirality : 0.043 0.154 1431 Planarity : 0.004 0.062 1536 Dihedral : 5.155 65.403 1275 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.37 % Allowed : 18.45 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.25), residues: 1183 helix: 1.07 (0.26), residues: 419 sheet: -1.17 (0.29), residues: 277 loop : -0.68 (0.30), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.005 0.001 HIS C 91 PHE 0.030 0.001 PHE H 212 TYR 0.016 0.002 TYR A 258 ARG 0.006 0.000 ARG C 304 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 449) hydrogen bonds : angle 5.20427 ( 1260) SS BOND : bond 0.00562 ( 6) SS BOND : angle 2.02452 ( 12) covalent geometry : bond 0.00332 ( 8826) covalent geometry : angle 0.61881 (12040) *********************** 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 152 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 ASP cc_start: 0.6889 (t0) cc_final: 0.6528 (t0) REVERT: A 290 TYR cc_start: 0.8183 (m-80) cc_final: 0.7764 (m-80) REVERT: B 309 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7153 (mt-10) REVERT: C 211 TRP cc_start: 0.6428 (OUTLIER) cc_final: 0.5619 (m-10) REVERT: G 42 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7361 (mm-30) REVERT: H 6 GLU cc_start: 0.4448 (mp0) cc_final: 0.4190 (mp0) REVERT: H 55 SER cc_start: 0.7853 (m) cc_final: 0.7434 (p) REVERT: H 192 MET cc_start: 0.6722 (tpp) cc_final: 0.6465 (tpp) outliers start: 36 outliers final: 32 residues processed: 144 average time/residue: 0.1974 time to fit residues: 40.1115 Evaluate side-chains 146 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 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 7 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 90 VAL 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 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 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain H residue 30 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 189 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 6 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 116 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4163 r_free = 0.4163 target = 0.135644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.114339 restraints weight = 17629.012| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.58 r_work: 0.3647 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8832 Z= 0.179 Angle : 0.660 9.385 12052 Z= 0.337 Chirality : 0.044 0.164 1431 Planarity : 0.004 0.061 1536 Dihedral : 5.282 66.142 1275 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 4.98 % Allowed : 17.96 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.25), residues: 1183 helix: 1.09 (0.26), residues: 412 sheet: -1.29 (0.29), residues: 277 loop : -0.64 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 82 HIS 0.006 0.001 HIS C 91 PHE 0.037 0.002 PHE H 212 TYR 0.020 0.002 TYR A 258 ARG 0.006 0.000 ARG C 304 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 449) hydrogen bonds : angle 5.32997 ( 1260) SS BOND : bond 0.00545 ( 6) SS BOND : angle 2.23168 ( 12) covalent geometry : bond 0.00425 ( 8826) covalent geometry : angle 0.65676 (12040) *********************** 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 155 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 114 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 74 ARG cc_start: 0.5843 (OUTLIER) cc_final: 0.5053 (mtt90) REVERT: C 211 TRP cc_start: 0.6468 (OUTLIER) cc_final: 0.5709 (m-10) REVERT: G 42 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7346 (mm-30) REVERT: H 50 TYR cc_start: 0.7634 (OUTLIER) cc_final: 0.6340 (t80) REVERT: H 55 SER cc_start: 0.7803 (OUTLIER) cc_final: 0.7412 (p) REVERT: H 192 MET cc_start: 0.6744 (tpp) cc_final: 0.6476 (tpp) outliers start: 41 outliers final: 34 residues processed: 145 average time/residue: 0.1946 time to fit residues: 39.4261 Evaluate side-chains 148 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 110 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 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 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 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 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 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 62 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 3 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.135978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.114695 restraints weight = 17620.210| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.53 r_work: 0.3645 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8832 Z= 0.192 Angle : 0.674 10.371 12052 Z= 0.344 Chirality : 0.044 0.169 1431 Planarity : 0.005 0.061 1536 Dihedral : 5.347 65.216 1275 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.73 % Allowed : 18.08 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1183 helix: 1.03 (0.26), residues: 413 sheet: -1.35 (0.29), residues: 277 loop : -0.65 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 82 HIS 0.007 0.001 HIS C 91 PHE 0.041 0.002 PHE H 212 TYR 0.023 0.002 TYR A 258 ARG 0.007 0.000 ARG C 304 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 449) hydrogen bonds : angle 5.40300 ( 1260) SS BOND : bond 0.00518 ( 6) SS BOND : angle 2.13686 ( 12) covalent geometry : bond 0.00458 ( 8826) covalent geometry : angle 0.67124 (12040) ********************** 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 150 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 111 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 74 ARG cc_start: 0.5732 (OUTLIER) cc_final: 0.4999 (mtt90) REVERT: C 211 TRP cc_start: 0.6470 (OUTLIER) cc_final: 0.5716 (m-10) REVERT: G 42 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7369 (mm-30) REVERT: H 50 TYR cc_start: 0.7642 (OUTLIER) cc_final: 0.6470 (t80) REVERT: H 55 SER cc_start: 0.7805 (m) cc_final: 0.7399 (p) REVERT: H 192 MET cc_start: 0.6777 (tpp) cc_final: 0.6535 (tpp) outliers start: 39 outliers final: 33 residues processed: 141 average time/residue: 0.1952 time to fit residues: 38.9718 Evaluate side-chains 147 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 111 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 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 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 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 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 97 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 58 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 42 optimal weight: 0.3980 chunk 24 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4162 r_free = 0.4162 target = 0.136199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.114743 restraints weight = 17470.119| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.59 r_work: 0.3645 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8832 Z= 0.180 Angle : 0.663 10.129 12052 Z= 0.338 Chirality : 0.044 0.165 1431 Planarity : 0.004 0.062 1536 Dihedral : 5.328 65.755 1275 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 4.61 % Allowed : 17.60 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.42 (0.25), residues: 1183 helix: 1.05 (0.26), residues: 414 sheet: -1.30 (0.30), residues: 272 loop : -0.70 (0.30), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 82 HIS 0.006 0.001 HIS C 91 PHE 0.040 0.002 PHE H 212 TYR 0.022 0.002 TYR A 258 ARG 0.006 0.000 ARG C 304 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 449) hydrogen bonds : angle 5.36928 ( 1260) SS BOND : bond 0.00520 ( 6) SS BOND : angle 2.12617 ( 12) covalent geometry : bond 0.00427 ( 8826) covalent geometry : angle 0.65975 (12040) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4980.99 seconds wall clock time: 87 minutes 59.49 seconds (5279.49 seconds total)