Starting phenix.real_space_refine on Wed Mar 4 09:08:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t96_25752/03_2026/7t96_25752.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t96_25752/03_2026/7t96_25752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t96_25752/03_2026/7t96_25752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t96_25752/03_2026/7t96_25752.map" model { file = "/net/cci-nas-00/data/ceres_data/7t96_25752/03_2026/7t96_25752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t96_25752/03_2026/7t96_25752.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4680 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 59 5.16 5 Cl 1 4.86 5 C 5382 2.51 5 N 1431 2.21 5 O 1577 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8450 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2015 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 12, 'TRANS': 261} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 4, 'TYR:plan': 2, 'ASP:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 81 Chain: "B" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1705 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2541 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 47 Chain: "D" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 403 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1747 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'2CU': 1, 'ACH': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.93, per 1000 atoms: 0.23 Number of scatterers: 8450 At special positions: 0 Unit cell: (91.8, 121.55, 124.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 59 16.00 O 1577 8.00 N 1431 7.00 C 5382 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 176 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 309.1 milliseconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2094 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 12 sheets defined 36.8% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 22 through 50 removed outlier: 3.557A pdb=" N ILE A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 55 removed outlier: 3.614A pdb=" N LEU A 54 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN A 55 " --> pdb=" O ARG A 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 51 through 55' Processing helix chain 'A' and resid 56 through 73 removed outlier: 3.703A pdb=" N TYR A 60 " --> pdb=" O THR A 56 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE A 61 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU A 62 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 65 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N CYS A 67 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 85 removed outlier: 3.827A pdb=" N VAL A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 94 removed outlier: 3.619A pdb=" N VAL A 94 " --> pdb=" O LEU A 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 91 through 94' Processing helix chain 'A' and resid 95 through 127 Processing helix chain 'A' and resid 130 through 135 removed outlier: 3.822A pdb=" N ARG A 135 " --> pdb=" O TYR A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 167 removed outlier: 3.653A pdb=" N ALA A 140 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) Proline residue: A 157 - end of helix removed outlier: 5.354A pdb=" N GLN A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N PHE A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 212 Proline residue: A 198 - end of helix Processing helix chain 'A' and resid 380 through 411 Proline residue: A 402 - end of helix removed outlier: 4.132A pdb=" N LEU A 408 " --> pdb=" O ASN A 404 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 442 removed outlier: 4.209A pdb=" N ILE A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR A 426 " --> pdb=" O TRP A 422 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER A 433 " --> pdb=" O CYS A 429 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 446 through 457 removed outlier: 3.516A pdb=" N THR A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 31 removed outlier: 4.442A pdb=" N ALA B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 removed outlier: 3.845A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 50 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN B 52 " --> pdb=" O THR B 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 45 through 52' Processing helix chain 'B' and resid 208 through 217 removed outlier: 3.711A pdb=" N LYS B 211 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ILE B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N HIS B 214 " --> pdb=" O LYS B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 256 Processing helix chain 'B' and resid 273 through 280 removed outlier: 4.246A pdb=" N LYS B 280 " --> pdb=" O GLY B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 296 through 310 removed outlier: 4.076A pdb=" N ALA B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 351 removed outlier: 3.765A pdb=" N VAL B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 26 Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.834A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.800A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 186 through 191 removed outlier: 3.519A pdb=" N PHE B 190 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 34 " --> pdb=" O HIS B 196 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B 38 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N ALA B 221 " --> pdb=" O ASP B 33 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LYS B 35 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE B 223 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU B 37 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N CYS B 225 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU B 39 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 8.978A pdb=" N ALA B 227 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE B 222 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N PHE B 268 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N PHE B 224 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASN B 270 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL B 226 " --> pdb=" O ASN B 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.568A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 7.090A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 70 " --> pdb=" O TRP C 82 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.844A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 153 removed outlier: 3.658A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 191 through 192 removed outlier: 3.505A pdb=" N SER C 191 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.522A pdb=" N ALA C 231 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.784A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASN C 293 " --> pdb=" O TYR C 289 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.530A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL E 37 " --> pdb=" O TYR E 95 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL E 97 " --> pdb=" O HIS E 35 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 146 through 149 removed outlier: 3.738A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 154 through 160 395 hydrogen bonds defined for protein. 1104 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.32 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1364 1.28 - 1.41: 2209 1.41 - 1.55: 4967 1.55 - 1.69: 2 1.69 - 1.83: 85 Bond restraints: 8627 Sorted by residual: bond pdb=" C01 2CU A 502 " pdb=" N02 2CU A 502 " ideal model delta sigma weight residual 1.445 1.257 0.188 2.00e-02 2.50e+03 8.81e+01 bond pdb=" C SER A 76 " pdb=" O SER A 76 " ideal model delta sigma weight residual 1.237 1.138 0.098 1.17e-02 7.31e+03 7.09e+01 bond pdb=" C TYR A 80 " pdb=" O TYR A 80 " ideal model delta sigma weight residual 1.236 1.152 0.084 1.26e-02 6.30e+03 4.44e+01 bond pdb=" C24 2CU A 502 " pdb=" N26 2CU A 502 " ideal model delta sigma weight residual 1.353 1.481 -0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C08 2CU A 502 " pdb=" N05 2CU A 502 " ideal model delta sigma weight residual 1.346 1.474 -0.128 2.00e-02 2.50e+03 4.08e+01 ... (remaining 8622 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 11399 2.40 - 4.81: 279 4.81 - 7.21: 50 7.21 - 9.61: 11 9.61 - 12.02: 7 Bond angle restraints: 11746 Sorted by residual: angle pdb=" N TYR A 80 " pdb=" CA TYR A 80 " pdb=" C TYR A 80 " ideal model delta sigma weight residual 111.82 99.80 12.02 1.16e+00 7.43e-01 1.07e+02 angle pdb=" N PRO A 418 " pdb=" CA PRO A 418 " pdb=" C PRO A 418 " ideal model delta sigma weight residual 113.53 101.66 11.87 1.39e+00 5.18e-01 7.29e+01 angle pdb=" N PHE A 61 " pdb=" CA PHE A 61 " pdb=" C PHE A 61 " ideal model delta sigma weight residual 112.54 102.43 10.11 1.22e+00 6.72e-01 6.87e+01 angle pdb=" N THR A 446 " pdb=" CA THR A 446 " pdb=" C THR A 446 " ideal model delta sigma weight residual 113.41 103.74 9.67 1.22e+00 6.72e-01 6.28e+01 angle pdb=" N THR A 420 " pdb=" CA THR A 420 " pdb=" C THR A 420 " ideal model delta sigma weight residual 114.62 106.97 7.65 1.14e+00 7.69e-01 4.51e+01 ... (remaining 11741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 4587 15.96 - 31.92: 358 31.92 - 47.88: 91 47.88 - 63.83: 14 63.83 - 79.79: 3 Dihedral angle restraints: 5053 sinusoidal: 1806 harmonic: 3247 Sorted by residual: dihedral pdb=" CB CYS A 96 " pdb=" SG CYS A 96 " pdb=" SG CYS A 176 " pdb=" CB CYS A 176 " ideal model delta sinusoidal sigma weight residual -86.00 -162.75 76.75 1 1.00e+01 1.00e-02 7.40e+01 dihedral pdb=" C ASP B 273 " pdb=" N ASP B 273 " pdb=" CA ASP B 273 " pdb=" CB ASP B 273 " ideal model delta harmonic sigma weight residual -122.60 -110.83 -11.77 0 2.50e+00 1.60e-01 2.22e+01 dihedral pdb=" CA GLN C 75 " pdb=" C GLN C 75 " pdb=" N ASP C 76 " pdb=" CA ASP C 76 " ideal model delta harmonic sigma weight residual 180.00 156.86 23.14 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 5050 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1195 0.080 - 0.159: 145 0.159 - 0.239: 19 0.239 - 0.319: 6 0.319 - 0.398: 4 Chirality restraints: 1369 Sorted by residual: chirality pdb=" CA ASP B 273 " pdb=" N ASP B 273 " pdb=" C ASP B 273 " pdb=" CB ASP B 273 " both_signs ideal model delta sigma weight residual False 2.51 2.91 -0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" CB VAL A 50 " pdb=" CA VAL A 50 " pdb=" CG1 VAL A 50 " pdb=" CG2 VAL A 50 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CA THR A 420 " pdb=" N THR A 420 " pdb=" C THR A 420 " pdb=" CB THR A 420 " both_signs ideal model delta sigma weight residual False 2.53 2.86 -0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 1366 not shown) Planarity restraints: 1479 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 409 " -0.017 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C ILE A 409 " 0.058 2.00e-02 2.50e+03 pdb=" O ILE A 409 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN A 410 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 49 " 0.016 2.00e-02 2.50e+03 3.14e-02 9.88e+00 pdb=" C LYS A 49 " -0.054 2.00e-02 2.50e+03 pdb=" O LYS A 49 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL A 50 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 58 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.58e+00 pdb=" C ASN A 58 " 0.051 2.00e-02 2.50e+03 pdb=" O ASN A 58 " -0.019 2.00e-02 2.50e+03 pdb=" N ASN A 59 " -0.017 2.00e-02 2.50e+03 ... (remaining 1476 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 163 2.65 - 3.21: 7904 3.21 - 3.78: 12292 3.78 - 4.34: 16635 4.34 - 4.90: 28016 Nonbonded interactions: 65010 Sorted by model distance: nonbonded pdb=" O ILE A 431 " pdb=" OG1 THR A 434 " model vdw 2.091 3.040 nonbonded pdb=" OG SER C 161 " pdb=" OD1 ASP C 163 " model vdw 2.125 3.040 nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.144 3.040 nonbonded pdb=" OG SER C 74 " pdb=" OD1 ASP C 76 " model vdw 2.179 3.040 nonbonded pdb=" OE2 GLU C 215 " pdb=" NH2 ARG C 219 " model vdw 2.220 3.120 ... (remaining 65005 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.670 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 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 : 0.008 0.188 8630 Z= 0.428 Angle : 0.940 12.018 11752 Z= 0.573 Chirality : 0.059 0.398 1369 Planarity : 0.005 0.058 1479 Dihedral : 12.639 79.793 2950 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.35 % Allowed : 1.15 % Favored : 98.50 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.25), residues: 1102 helix: 0.82 (0.28), residues: 349 sheet: -0.57 (0.32), residues: 269 loop : -1.82 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 135 TYR 0.019 0.002 TYR E 94 PHE 0.018 0.002 PHE E 68 TRP 0.042 0.003 TRP A 99 HIS 0.006 0.002 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00799 ( 8627) covalent geometry : angle 0.93938 (11746) SS BOND : bond 0.01002 ( 3) SS BOND : angle 1.52239 ( 6) hydrogen bonds : bond 0.15791 ( 395) hydrogen bonds : angle 6.57688 ( 1104) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 250 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 33 LEU cc_start: 0.8979 (mt) cc_final: 0.8738 (mp) REVERT: A 177 TYR cc_start: 0.7169 (p90) cc_final: 0.6855 (p90) REVERT: A 397 ILE cc_start: 0.8301 (mm) cc_final: 0.8087 (tt) REVERT: A 404 ASN cc_start: 0.8666 (m-40) cc_final: 0.8289 (m-40) REVERT: B 218 ASP cc_start: 0.7088 (t0) cc_final: 0.6848 (t0) REVERT: B 247 SER cc_start: 0.7795 (m) cc_final: 0.7535 (t) REVERT: B 250 LEU cc_start: 0.8012 (tp) cc_final: 0.7789 (tt) REVERT: B 272 LYS cc_start: 0.8563 (pttt) cc_final: 0.8238 (ttpt) REVERT: B 351 CYS cc_start: 0.7712 (m) cc_final: 0.7507 (m) REVERT: C 49 ARG cc_start: 0.7909 (mmt-90) cc_final: 0.7558 (mpt180) REVERT: C 198 LEU cc_start: 0.8466 (pt) cc_final: 0.8185 (pp) REVERT: C 239 ASN cc_start: 0.7623 (m-40) cc_final: 0.6461 (t0) REVERT: C 290 ASP cc_start: 0.6860 (m-30) cc_final: 0.6627 (m-30) outliers start: 3 outliers final: 3 residues processed: 250 average time/residue: 0.0905 time to fit residues: 30.3696 Evaluate side-chains 221 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 218 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 420 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 51 ASN B 194 ASN B 322 HIS ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN E 142 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.123577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.109273 restraints weight = 13537.822| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.22 r_work: 0.3329 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8630 Z= 0.200 Angle : 0.702 11.652 11752 Z= 0.361 Chirality : 0.047 0.222 1369 Planarity : 0.005 0.063 1479 Dihedral : 5.749 57.996 1217 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.19 % Allowed : 13.94 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.26), residues: 1102 helix: 1.72 (0.29), residues: 340 sheet: -0.48 (0.32), residues: 276 loop : -1.74 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 52 TYR 0.018 0.002 TYR E 94 PHE 0.028 0.002 PHE A 181 TRP 0.014 0.002 TRP A 99 HIS 0.005 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 8627) covalent geometry : angle 0.70170 (11746) SS BOND : bond 0.00968 ( 3) SS BOND : angle 1.39684 ( 6) hydrogen bonds : bond 0.05284 ( 395) hydrogen bonds : angle 5.16853 ( 1104) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 226 time to evaluate : 0.289 Fit side-chains REVERT: A 33 LEU cc_start: 0.9078 (mt) cc_final: 0.8723 (mp) REVERT: A 62 LEU cc_start: 0.8355 (tp) cc_final: 0.8107 (tp) REVERT: B 193 LYS cc_start: 0.8817 (tppp) cc_final: 0.8615 (tppp) REVERT: B 218 ASP cc_start: 0.7601 (t0) cc_final: 0.7364 (t0) REVERT: B 247 SER cc_start: 0.7956 (m) cc_final: 0.7740 (t) REVERT: B 250 LEU cc_start: 0.8245 (tp) cc_final: 0.8011 (tt) REVERT: B 272 LYS cc_start: 0.8891 (pttt) cc_final: 0.8499 (ttpt) REVERT: B 274 LEU cc_start: 0.8301 (tt) cc_final: 0.8049 (tt) REVERT: B 278 LYS cc_start: 0.8603 (ttmt) cc_final: 0.8382 (ttmm) REVERT: B 343 ILE cc_start: 0.8529 (mm) cc_final: 0.8281 (mt) REVERT: B 351 CYS cc_start: 0.8337 (m) cc_final: 0.8120 (m) REVERT: C 49 ARG cc_start: 0.8403 (mmt-90) cc_final: 0.8081 (mpt180) REVERT: C 198 LEU cc_start: 0.8573 (pt) cc_final: 0.8320 (pp) REVERT: C 239 ASN cc_start: 0.7990 (m-40) cc_final: 0.6735 (t0) REVERT: C 290 ASP cc_start: 0.7485 (m-30) cc_final: 0.7259 (m-30) REVERT: E 140 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.7896 (mtm) REVERT: E 146 SER cc_start: 0.8512 (p) cc_final: 0.8248 (t) outliers start: 19 outliers final: 13 residues processed: 235 average time/residue: 0.0885 time to fit residues: 28.3419 Evaluate side-chains 234 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 220 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 174 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 102 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 78 optimal weight: 0.0970 chunk 57 optimal weight: 0.9990 chunk 48 optimal weight: 0.0970 chunk 104 optimal weight: 0.9990 overall best weight: 0.5976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN E 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.124821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.110495 restraints weight = 13491.969| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.22 r_work: 0.3355 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8630 Z= 0.147 Angle : 0.634 10.976 11752 Z= 0.325 Chirality : 0.044 0.198 1369 Planarity : 0.004 0.061 1479 Dihedral : 5.204 58.546 1214 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.88 % Allowed : 17.17 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.26), residues: 1102 helix: 2.07 (0.29), residues: 339 sheet: -0.41 (0.32), residues: 282 loop : -1.57 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 202 TYR 0.018 0.001 TYR E 190 PHE 0.022 0.001 PHE A 195 TRP 0.013 0.001 TRP A 155 HIS 0.004 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 8627) covalent geometry : angle 0.63397 (11746) SS BOND : bond 0.00749 ( 3) SS BOND : angle 1.09063 ( 6) hydrogen bonds : bond 0.04500 ( 395) hydrogen bonds : angle 4.84211 ( 1104) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 214 time to evaluate : 0.297 Fit side-chains REVERT: A 33 LEU cc_start: 0.9031 (mt) cc_final: 0.8809 (mp) REVERT: A 62 LEU cc_start: 0.8310 (tp) cc_final: 0.8098 (tp) REVERT: A 100 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6713 (tp) REVERT: A 114 LEU cc_start: 0.8226 (mt) cc_final: 0.7717 (mp) REVERT: A 404 ASN cc_start: 0.8918 (m110) cc_final: 0.8505 (m-40) REVERT: B 193 LYS cc_start: 0.8836 (tppp) cc_final: 0.8571 (tppp) REVERT: B 218 ASP cc_start: 0.7587 (t0) cc_final: 0.7329 (t0) REVERT: B 250 LEU cc_start: 0.8231 (tp) cc_final: 0.8018 (tt) REVERT: B 272 LYS cc_start: 0.8872 (pttt) cc_final: 0.8532 (ttpt) REVERT: B 343 ILE cc_start: 0.8545 (mm) cc_final: 0.8298 (mt) REVERT: C 81 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.7264 (mt) REVERT: C 198 LEU cc_start: 0.8536 (pt) cc_final: 0.8333 (pp) REVERT: C 219 ARG cc_start: 0.8282 (mmt-90) cc_final: 0.8000 (mmt-90) REVERT: C 239 ASN cc_start: 0.7929 (m-40) cc_final: 0.6692 (t0) REVERT: C 290 ASP cc_start: 0.7478 (m-30) cc_final: 0.7273 (m-30) REVERT: E 101 TYR cc_start: 0.8095 (m-80) cc_final: 0.7729 (m-80) REVERT: E 178 LEU cc_start: 0.8585 (tp) cc_final: 0.8348 (tp) outliers start: 25 outliers final: 12 residues processed: 227 average time/residue: 0.0904 time to fit residues: 27.8508 Evaluate side-chains 221 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 207 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 174 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 31 optimal weight: 0.7980 chunk 52 optimal weight: 0.0770 chunk 56 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 90 optimal weight: 0.0870 chunk 94 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 176 GLN C 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.124900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.110429 restraints weight = 13786.824| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.26 r_work: 0.3356 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8630 Z= 0.133 Angle : 0.614 11.148 11752 Z= 0.315 Chirality : 0.044 0.208 1369 Planarity : 0.004 0.063 1479 Dihedral : 4.992 57.021 1214 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.00 % Allowed : 18.89 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.26), residues: 1102 helix: 2.22 (0.29), residues: 342 sheet: -0.45 (0.31), residues: 283 loop : -1.52 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 52 TYR 0.018 0.001 TYR E 190 PHE 0.021 0.001 PHE A 195 TRP 0.012 0.001 TRP C 82 HIS 0.004 0.001 HIS B 196 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8627) covalent geometry : angle 0.61410 (11746) SS BOND : bond 0.00697 ( 3) SS BOND : angle 1.00704 ( 6) hydrogen bonds : bond 0.04189 ( 395) hydrogen bonds : angle 4.72841 ( 1104) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 0.312 Fit side-chains REVERT: A 62 LEU cc_start: 0.8317 (tp) cc_final: 0.8090 (tp) REVERT: A 389 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8083 (mt) REVERT: A 450 THR cc_start: 0.8567 (OUTLIER) cc_final: 0.8325 (p) REVERT: B 193 LYS cc_start: 0.8875 (tppp) cc_final: 0.8598 (tppp) REVERT: B 218 ASP cc_start: 0.7582 (t0) cc_final: 0.7358 (t0) REVERT: B 272 LYS cc_start: 0.8828 (pttt) cc_final: 0.8522 (ttpt) REVERT: B 343 ILE cc_start: 0.8538 (mm) cc_final: 0.8290 (mt) REVERT: C 81 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.7238 (mt) REVERT: C 219 ARG cc_start: 0.8279 (mmt-90) cc_final: 0.7987 (mmt-90) REVERT: C 239 ASN cc_start: 0.7876 (m110) cc_final: 0.6575 (t0) REVERT: C 290 ASP cc_start: 0.7491 (m-30) cc_final: 0.7276 (m-30) REVERT: C 304 ARG cc_start: 0.8015 (ttp80) cc_final: 0.7794 (ttp-170) REVERT: E 91 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8575 (p) REVERT: E 97 VAL cc_start: 0.7775 (OUTLIER) cc_final: 0.7265 (t) REVERT: E 101 TYR cc_start: 0.8020 (m-80) cc_final: 0.7569 (m-80) REVERT: E 140 MET cc_start: 0.8595 (mtm) cc_final: 0.8226 (mtt) outliers start: 26 outliers final: 16 residues processed: 228 average time/residue: 0.0920 time to fit residues: 28.4995 Evaluate side-chains 225 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 174 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 14 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 76 optimal weight: 0.2980 chunk 104 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.125096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.110518 restraints weight = 13685.639| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.26 r_work: 0.3351 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8630 Z= 0.148 Angle : 0.634 11.041 11752 Z= 0.320 Chirality : 0.044 0.189 1369 Planarity : 0.004 0.066 1479 Dihedral : 4.964 56.243 1214 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.80 % Allowed : 18.43 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.26), residues: 1102 helix: 2.17 (0.30), residues: 345 sheet: -0.38 (0.31), residues: 281 loop : -1.44 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 52 TYR 0.018 0.001 TYR E 190 PHE 0.024 0.001 PHE A 195 TRP 0.012 0.001 TRP C 82 HIS 0.004 0.001 HIS B 196 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8627) covalent geometry : angle 0.63370 (11746) SS BOND : bond 0.00749 ( 3) SS BOND : angle 1.04928 ( 6) hydrogen bonds : bond 0.04358 ( 395) hydrogen bonds : angle 4.69665 ( 1104) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 0.252 Fit side-chains REVERT: A 43 LEU cc_start: 0.7667 (mt) cc_final: 0.7427 (mt) REVERT: A 389 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8091 (mt) REVERT: A 403 TYR cc_start: 0.7584 (t80) cc_final: 0.7295 (t80) REVERT: A 404 ASN cc_start: 0.8901 (m110) cc_final: 0.8525 (m-40) REVERT: A 450 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8332 (p) REVERT: B 193 LYS cc_start: 0.8870 (tppp) cc_final: 0.8583 (tppp) REVERT: B 218 ASP cc_start: 0.7583 (t0) cc_final: 0.7353 (t0) REVERT: B 272 LYS cc_start: 0.8825 (pttt) cc_final: 0.8538 (ttpt) REVERT: B 343 ILE cc_start: 0.8545 (mm) cc_final: 0.8307 (mt) REVERT: C 49 ARG cc_start: 0.8421 (mmt-90) cc_final: 0.8139 (mmt-90) REVERT: C 81 ILE cc_start: 0.7572 (OUTLIER) cc_final: 0.7266 (mt) REVERT: C 239 ASN cc_start: 0.7903 (m110) cc_final: 0.6600 (t0) REVERT: E 91 THR cc_start: 0.8795 (OUTLIER) cc_final: 0.8576 (p) REVERT: E 97 VAL cc_start: 0.7832 (OUTLIER) cc_final: 0.7322 (t) REVERT: E 101 TYR cc_start: 0.8060 (m-80) cc_final: 0.7617 (m-80) REVERT: E 237 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8335 (mp) outliers start: 33 outliers final: 19 residues processed: 222 average time/residue: 0.0862 time to fit residues: 26.5671 Evaluate side-chains 223 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 237 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 81 optimal weight: 20.0000 chunk 14 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 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 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.123458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.108920 restraints weight = 13613.090| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.24 r_work: 0.3334 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8630 Z= 0.180 Angle : 0.657 10.910 11752 Z= 0.334 Chirality : 0.045 0.221 1369 Planarity : 0.005 0.069 1479 Dihedral : 5.093 56.423 1214 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 4.38 % Allowed : 19.47 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.26), residues: 1102 helix: 2.13 (0.30), residues: 345 sheet: -0.41 (0.31), residues: 283 loop : -1.44 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 96 TYR 0.019 0.002 TYR E 190 PHE 0.021 0.002 PHE A 195 TRP 0.012 0.002 TRP C 82 HIS 0.004 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 8627) covalent geometry : angle 0.65615 (11746) SS BOND : bond 0.00867 ( 3) SS BOND : angle 1.25864 ( 6) hydrogen bonds : bond 0.04702 ( 395) hydrogen bonds : angle 4.76513 ( 1104) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 207 time to evaluate : 0.282 Fit side-chains REVERT: A 43 LEU cc_start: 0.7688 (mt) cc_final: 0.7421 (mt) REVERT: A 393 LEU cc_start: 0.7803 (tp) cc_final: 0.7561 (tt) REVERT: A 403 TYR cc_start: 0.7594 (t80) cc_final: 0.7389 (t80) REVERT: B 193 LYS cc_start: 0.8856 (tppp) cc_final: 0.8566 (tppp) REVERT: B 211 LYS cc_start: 0.8730 (mmtt) cc_final: 0.8500 (mmmt) REVERT: B 218 ASP cc_start: 0.7619 (t0) cc_final: 0.7369 (t0) REVERT: B 272 LYS cc_start: 0.8837 (pttt) cc_final: 0.8559 (ttpt) REVERT: B 343 ILE cc_start: 0.8541 (mm) cc_final: 0.8300 (mt) REVERT: C 52 ARG cc_start: 0.7971 (ptp90) cc_final: 0.7676 (ptp90) REVERT: C 81 ILE cc_start: 0.7597 (OUTLIER) cc_final: 0.7309 (mt) REVERT: C 239 ASN cc_start: 0.7968 (m-40) cc_final: 0.6682 (t0) REVERT: E 91 THR cc_start: 0.8847 (OUTLIER) cc_final: 0.8604 (p) REVERT: E 97 VAL cc_start: 0.7857 (OUTLIER) cc_final: 0.7380 (t) REVERT: E 101 TYR cc_start: 0.8116 (m-80) cc_final: 0.7878 (m-80) REVERT: E 140 MET cc_start: 0.8605 (mtm) cc_final: 0.8390 (mtm) REVERT: E 237 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8319 (mp) outliers start: 38 outliers final: 25 residues processed: 230 average time/residue: 0.0772 time to fit residues: 24.8872 Evaluate side-chains 236 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 207 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 237 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 70 optimal weight: 1.9990 chunk 75 optimal weight: 0.3980 chunk 102 optimal weight: 0.0970 chunk 32 optimal weight: 0.3980 chunk 14 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 GLN C 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.126129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.111433 restraints weight = 13736.607| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.28 r_work: 0.3361 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8630 Z= 0.122 Angle : 0.624 10.824 11752 Z= 0.315 Chirality : 0.043 0.226 1369 Planarity : 0.004 0.069 1479 Dihedral : 4.899 55.537 1214 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.46 % Allowed : 21.08 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.26), residues: 1102 helix: 2.20 (0.30), residues: 347 sheet: -0.35 (0.31), residues: 282 loop : -1.35 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 96 TYR 0.016 0.001 TYR E 190 PHE 0.025 0.001 PHE A 195 TRP 0.013 0.001 TRP C 82 HIS 0.004 0.001 HIS B 196 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8627) covalent geometry : angle 0.62398 (11746) SS BOND : bond 0.00643 ( 3) SS BOND : angle 0.86366 ( 6) hydrogen bonds : bond 0.04019 ( 395) hydrogen bonds : angle 4.59865 ( 1104) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 404 ASN cc_start: 0.8910 (m110) cc_final: 0.8500 (m-40) REVERT: A 450 THR cc_start: 0.8558 (OUTLIER) cc_final: 0.8328 (p) REVERT: B 218 ASP cc_start: 0.7596 (t0) cc_final: 0.7373 (t0) REVERT: B 272 LYS cc_start: 0.8804 (pttt) cc_final: 0.8539 (ttpt) REVERT: B 343 ILE cc_start: 0.8553 (mm) cc_final: 0.8308 (mt) REVERT: C 81 ILE cc_start: 0.7540 (OUTLIER) cc_final: 0.7183 (mt) REVERT: C 246 ASP cc_start: 0.7764 (t70) cc_final: 0.7314 (t0) REVERT: E 97 VAL cc_start: 0.7763 (OUTLIER) cc_final: 0.7256 (t) REVERT: E 101 TYR cc_start: 0.8000 (m-80) cc_final: 0.7558 (m-80) REVERT: E 140 MET cc_start: 0.8578 (mtm) cc_final: 0.8198 (mtt) REVERT: E 213 THR cc_start: 0.8691 (t) cc_final: 0.8316 (p) outliers start: 30 outliers final: 17 residues processed: 223 average time/residue: 0.0768 time to fit residues: 24.0309 Evaluate side-chains 220 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 97 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 83 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 101 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.122887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.108247 restraints weight = 13540.880| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.25 r_work: 0.3322 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 8630 Z= 0.211 Angle : 0.688 10.667 11752 Z= 0.349 Chirality : 0.046 0.235 1369 Planarity : 0.005 0.075 1479 Dihedral : 5.214 56.584 1214 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.00 % Allowed : 21.77 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.26), residues: 1102 helix: 2.04 (0.29), residues: 349 sheet: -0.39 (0.33), residues: 270 loop : -1.48 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 52 TYR 0.020 0.002 TYR E 190 PHE 0.023 0.002 PHE A 195 TRP 0.017 0.002 TRP A 148 HIS 0.004 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00487 ( 8627) covalent geometry : angle 0.68769 (11746) SS BOND : bond 0.00969 ( 3) SS BOND : angle 1.32484 ( 6) hydrogen bonds : bond 0.05008 ( 395) hydrogen bonds : angle 4.81808 ( 1104) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 212 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 404 ASN cc_start: 0.8923 (m110) cc_final: 0.8490 (m-40) REVERT: B 218 ASP cc_start: 0.7677 (t0) cc_final: 0.7425 (t0) REVERT: B 272 LYS cc_start: 0.8853 (pttt) cc_final: 0.8596 (ttpt) REVERT: B 343 ILE cc_start: 0.8545 (mm) cc_final: 0.8304 (mt) REVERT: C 81 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7314 (mt) REVERT: E 97 VAL cc_start: 0.7821 (OUTLIER) cc_final: 0.7363 (t) REVERT: E 101 TYR cc_start: 0.8171 (m-80) cc_final: 0.7965 (m-80) REVERT: E 222 GLU cc_start: 0.7228 (tm-30) cc_final: 0.7025 (tm-30) outliers start: 26 outliers final: 20 residues processed: 228 average time/residue: 0.0832 time to fit residues: 26.3787 Evaluate side-chains 231 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 209 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 230 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 95 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 54 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 0.0170 chunk 38 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 32 optimal weight: 0.0470 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.126229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.111496 restraints weight = 13673.003| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.28 r_work: 0.3369 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8630 Z= 0.118 Angle : 0.625 10.075 11752 Z= 0.315 Chirality : 0.043 0.240 1369 Planarity : 0.004 0.074 1479 Dihedral : 4.830 46.863 1213 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.19 % Allowed : 22.81 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.26), residues: 1102 helix: 2.24 (0.30), residues: 346 sheet: -0.32 (0.32), residues: 277 loop : -1.38 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 96 TYR 0.016 0.001 TYR E 190 PHE 0.022 0.001 PHE A 195 TRP 0.018 0.001 TRP A 148 HIS 0.004 0.001 HIS B 196 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 8627) covalent geometry : angle 0.62487 (11746) SS BOND : bond 0.00577 ( 3) SS BOND : angle 0.82913 ( 6) hydrogen bonds : bond 0.03914 ( 395) hydrogen bonds : angle 4.58237 ( 1104) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 200 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 393 LEU cc_start: 0.7749 (tp) cc_final: 0.7495 (tt) REVERT: A 404 ASN cc_start: 0.8887 (m110) cc_final: 0.8509 (m-40) REVERT: A 450 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8334 (p) REVERT: B 218 ASP cc_start: 0.7584 (t0) cc_final: 0.7360 (t0) REVERT: B 272 LYS cc_start: 0.8790 (pttt) cc_final: 0.8544 (ttpt) REVERT: B 343 ILE cc_start: 0.8566 (mm) cc_final: 0.8316 (mt) REVERT: C 81 ILE cc_start: 0.7546 (OUTLIER) cc_final: 0.7190 (mt) REVERT: C 246 ASP cc_start: 0.7745 (t70) cc_final: 0.7304 (t0) REVERT: E 97 VAL cc_start: 0.7739 (OUTLIER) cc_final: 0.7231 (t) REVERT: E 101 TYR cc_start: 0.7986 (m-80) cc_final: 0.7560 (m-80) REVERT: E 213 THR cc_start: 0.8678 (t) cc_final: 0.8329 (p) outliers start: 19 outliers final: 12 residues processed: 214 average time/residue: 0.0886 time to fit residues: 26.0567 Evaluate side-chains 211 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 196 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 174 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 76 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 43 optimal weight: 0.5980 chunk 11 optimal weight: 0.4980 chunk 26 optimal weight: 0.0980 chunk 81 optimal weight: 30.0000 chunk 99 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN C 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.126312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.111640 restraints weight = 13634.000| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.27 r_work: 0.3373 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8630 Z= 0.126 Angle : 0.637 11.609 11752 Z= 0.319 Chirality : 0.043 0.226 1369 Planarity : 0.004 0.066 1479 Dihedral : 4.814 54.584 1213 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.30 % Allowed : 22.93 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.26), residues: 1102 helix: 2.22 (0.30), residues: 350 sheet: -0.42 (0.31), residues: 285 loop : -1.34 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 96 TYR 0.019 0.001 TYR E 190 PHE 0.023 0.001 PHE A 195 TRP 0.023 0.001 TRP A 148 HIS 0.004 0.001 HIS B 196 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8627) covalent geometry : angle 0.63729 (11746) SS BOND : bond 0.00637 ( 3) SS BOND : angle 0.84627 ( 6) hydrogen bonds : bond 0.03996 ( 395) hydrogen bonds : angle 4.54566 ( 1104) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 393 LEU cc_start: 0.7732 (tp) cc_final: 0.7457 (tt) REVERT: A 404 ASN cc_start: 0.8885 (m110) cc_final: 0.8524 (m-40) REVERT: B 218 ASP cc_start: 0.7608 (t0) cc_final: 0.7362 (t0) REVERT: B 272 LYS cc_start: 0.8778 (pttt) cc_final: 0.8541 (ttpt) REVERT: B 343 ILE cc_start: 0.8567 (mm) cc_final: 0.8317 (mt) REVERT: C 81 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.7207 (mt) REVERT: C 246 ASP cc_start: 0.7799 (t70) cc_final: 0.7335 (t0) REVERT: E 97 VAL cc_start: 0.7751 (OUTLIER) cc_final: 0.7252 (t) REVERT: E 101 TYR cc_start: 0.8017 (m-80) cc_final: 0.7565 (m-80) REVERT: E 140 MET cc_start: 0.8567 (mtm) cc_final: 0.8231 (mtt) outliers start: 20 outliers final: 13 residues processed: 213 average time/residue: 0.0885 time to fit residues: 25.8615 Evaluate side-chains 216 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 201 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 58 optimal weight: 0.7980 chunk 42 optimal weight: 0.1980 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.0170 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 44 optimal weight: 0.0570 chunk 29 optimal weight: 1.9990 chunk 81 optimal weight: 30.0000 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN C 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.127296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.112580 restraints weight = 13577.958| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.27 r_work: 0.3383 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8630 Z= 0.120 Angle : 0.642 17.650 11752 Z= 0.318 Chirality : 0.044 0.247 1369 Planarity : 0.004 0.068 1479 Dihedral : 4.960 73.981 1213 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.19 % Allowed : 23.27 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.26), residues: 1102 helix: 2.19 (0.29), residues: 351 sheet: -0.40 (0.31), residues: 283 loop : -1.26 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 96 TYR 0.020 0.001 TYR E 190 PHE 0.022 0.001 PHE A 195 TRP 0.025 0.001 TRP A 148 HIS 0.004 0.001 HIS B 196 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8627) covalent geometry : angle 0.64209 (11746) SS BOND : bond 0.00574 ( 3) SS BOND : angle 0.79007 ( 6) hydrogen bonds : bond 0.03849 ( 395) hydrogen bonds : angle 4.50966 ( 1104) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2433.71 seconds wall clock time: 42 minutes 16.85 seconds (2536.85 seconds total)