Starting phenix.real_space_refine on Wed Jun 11 04:20:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t96_25752/06_2025/7t96_25752.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t96_25752/06_2025/7t96_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_25752/06_2025/7t96_25752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t96_25752/06_2025/7t96_25752.map" model { file = "/net/cci-nas-00/data/ceres_data/7t96_25752/06_2025/7t96_25752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t96_25752/06_2025/7t96_25752.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 2} 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: {'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ARG:plan': 2} 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, 'ARG:plan': 2, 'ASP:plan': 1} 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: 5.83, per 1000 atoms: 0.69 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: 2.38 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.00 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: 2.59 Time building geometry restraints manager: 2.80 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.840 Find NCS groups from input model: 0.100 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.040 ------------------------------------------------------------------------------- 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 : 11.18 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 (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: -0.99 (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 TRP 0.042 0.003 TRP A 99 HIS 0.006 0.002 HIS B 189 PHE 0.018 0.002 PHE E 68 TYR 0.019 0.002 TYR E 94 ARG 0.004 0.001 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.15791 ( 395) hydrogen bonds : angle 6.57688 ( 1104) SS BOND : bond 0.01002 ( 3) SS BOND : angle 1.52239 ( 6) covalent geometry : bond 0.00799 ( 8627) covalent geometry : angle 0.93938 (11746) *********************** 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 : 0.985 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: 0.6856 (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: 0.6847 (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: 0.2145 time to fit residues: 72.1927 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 : 0.864 ------------------------------------------------------------------------------- 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 92 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 44 optimal weight: 0.1980 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 C 110 ASN E 142 GLN E 194 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.125475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.111211 restraints weight = 13324.571| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.20 r_work: 0.3366 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1461 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= 0.146 Angle : 0.665 11.406 11752 Z= 0.340 Chirality : 0.045 0.215 1369 Planarity : 0.004 0.060 1479 Dihedral : 5.592 59.610 1217 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.84 % Allowed : 14.17 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.26), residues: 1102 helix: 1.82 (0.29), residues: 339 sheet: -0.46 (0.32), residues: 281 loop : -1.74 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 212 HIS 0.004 0.001 HIS B 189 PHE 0.027 0.001 PHE A 181 TYR 0.016 0.001 TYR E 190 ARG 0.003 0.000 ARG C 52 Details of bonding type rmsd hydrogen bonds : bond 0.04630 ( 395) hydrogen bonds : angle 5.02943 ( 1104) SS BOND : bond 0.00722 ( 3) SS BOND : angle 1.13270 ( 6) covalent geometry : bond 0.00326 ( 8627) covalent geometry : angle 0.66509 (11746) *********************** 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 234 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 218 time to evaluate : 0.877 Fit side-chains REVERT: A 33 LEU cc_start: 0.9043 (mt) cc_final: 0.8690 (mp) REVERT: A 62 LEU cc_start: 0.8303 (tp) cc_final: 0.8046 (tp) REVERT: A 404 ASN cc_start: 0.8876 (m-40) cc_final: 0.8440 (m-40) REVERT: B 218 ASP cc_start: 0.7560 (t0) cc_final: 0.7316 (t0) REVERT: B 247 SER cc_start: 0.7928 (m) cc_final: 0.7719 (t) REVERT: B 250 LEU cc_start: 0.8241 (tp) cc_final: 0.8036 (tt) REVERT: B 272 LYS cc_start: 0.8865 (pttt) cc_final: 0.8486 (ttpt) REVERT: B 343 ILE cc_start: 0.8533 (mm) cc_final: 0.8272 (mt) REVERT: C 49 ARG cc_start: 0.8377 (mmt-90) cc_final: 0.8031 (mpt180) REVERT: C 198 LEU cc_start: 0.8537 (pt) cc_final: 0.8319 (pp) REVERT: C 239 ASN cc_start: 0.7946 (m-40) cc_final: 0.6717 (t0) REVERT: C 290 ASP cc_start: 0.7417 (m-30) cc_final: 0.7152 (m-30) REVERT: E 91 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8583 (p) REVERT: E 101 TYR cc_start: 0.7981 (m-80) cc_final: 0.7726 (m-80) outliers start: 16 outliers final: 11 residues processed: 226 average time/residue: 0.2112 time to fit residues: 64.6904 Evaluate side-chains 223 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 211 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 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 174 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 77 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 12 optimal weight: 0.2980 chunk 56 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.125155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.110652 restraints weight = 13668.439| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.25 r_work: 0.3355 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1749 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= 0.142 Angle : 0.628 10.992 11752 Z= 0.322 Chirality : 0.044 0.191 1369 Planarity : 0.004 0.062 1479 Dihedral : 5.117 56.313 1214 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.53 % Allowed : 17.51 % 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 (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: -0.16 (0.26), residues: 1102 helix: 2.09 (0.29), residues: 338 sheet: -0.37 (0.32), residues: 280 loop : -1.58 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 212 HIS 0.004 0.001 HIS B 189 PHE 0.021 0.001 PHE A 195 TYR 0.018 0.001 TYR E 190 ARG 0.007 0.000 ARG E 202 Details of bonding type rmsd hydrogen bonds : bond 0.04430 ( 395) hydrogen bonds : angle 4.79379 ( 1104) SS BOND : bond 0.00743 ( 3) SS BOND : angle 1.11901 ( 6) covalent geometry : bond 0.00316 ( 8627) covalent geometry : angle 0.62753 (11746) *********************** 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: 22 poor density : 217 time to evaluate : 0.925 Fit side-chains REVERT: A 62 LEU cc_start: 0.8305 (tp) cc_final: 0.8075 (tp) REVERT: A 114 LEU cc_start: 0.8227 (mt) cc_final: 0.7859 (mp) REVERT: B 218 ASP cc_start: 0.7543 (t0) cc_final: 0.7302 (t0) REVERT: B 250 LEU cc_start: 0.8237 (tp) cc_final: 0.8015 (tt) REVERT: B 272 LYS cc_start: 0.8859 (pttt) cc_final: 0.8481 (ttpt) REVERT: B 343 ILE cc_start: 0.8539 (mm) cc_final: 0.8287 (mt) REVERT: C 49 ARG cc_start: 0.8352 (mmt-90) cc_final: 0.8016 (mpt180) REVERT: C 81 ILE cc_start: 0.7546 (OUTLIER) cc_final: 0.7228 (mt) REVERT: C 219 ARG cc_start: 0.8259 (mmt-90) cc_final: 0.7977 (mmt-90) REVERT: C 239 ASN cc_start: 0.7910 (m-40) cc_final: 0.6817 (t0) REVERT: C 290 ASP cc_start: 0.7448 (m-30) cc_final: 0.7229 (m-30) REVERT: E 101 TYR cc_start: 0.8082 (m-80) cc_final: 0.7683 (m-80) REVERT: E 140 MET cc_start: 0.8641 (mtm) cc_final: 0.8245 (mtt) REVERT: E 178 LEU cc_start: 0.8581 (tp) cc_final: 0.8348 (tp) outliers start: 22 outliers final: 12 residues processed: 230 average time/residue: 0.2094 time to fit residues: 65.3163 Evaluate side-chains 226 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 213 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 457 CYS 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 317 CYS Chi-restraints excluded: chain C residue 318 LEU 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 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 37 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.123622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.109260 restraints weight = 13526.248| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.22 r_work: 0.3335 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1876 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= 0.175 Angle : 0.643 11.216 11752 Z= 0.330 Chirality : 0.045 0.212 1369 Planarity : 0.004 0.065 1479 Dihedral : 5.122 57.243 1214 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.92 % Allowed : 17.86 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.12 (0.26), residues: 1102 helix: 2.16 (0.30), residues: 338 sheet: -0.42 (0.31), residues: 283 loop : -1.53 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 339 HIS 0.004 0.001 HIS B 189 PHE 0.024 0.002 PHE A 195 TYR 0.020 0.002 TYR E 190 ARG 0.007 0.000 ARG E 202 Details of bonding type rmsd hydrogen bonds : bond 0.04732 ( 395) hydrogen bonds : angle 4.82444 ( 1104) SS BOND : bond 0.00847 ( 3) SS BOND : angle 1.20864 ( 6) covalent geometry : bond 0.00399 ( 8627) covalent geometry : angle 0.64233 (11746) *********************** 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 240 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 206 time to evaluate : 1.248 Fit side-chains REVERT: A 43 LEU cc_start: 0.7699 (mt) cc_final: 0.7433 (mt) REVERT: A 62 LEU cc_start: 0.8327 (tp) cc_final: 0.8095 (tp) REVERT: A 389 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8094 (tp) REVERT: A 393 LEU cc_start: 0.7810 (tp) cc_final: 0.7579 (tt) REVERT: B 218 ASP cc_start: 0.7606 (t0) cc_final: 0.7367 (t0) REVERT: B 250 LEU cc_start: 0.8282 (tp) cc_final: 0.8064 (tt) REVERT: B 272 LYS cc_start: 0.8852 (pttt) cc_final: 0.8551 (ttpt) REVERT: B 343 ILE cc_start: 0.8533 (mm) cc_final: 0.8294 (mt) REVERT: C 52 ARG cc_start: 0.7987 (ptp90) cc_final: 0.7393 (ptp90) REVERT: C 81 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7285 (mt) REVERT: C 239 ASN cc_start: 0.7908 (m-40) cc_final: 0.6646 (t0) REVERT: E 91 THR cc_start: 0.8839 (OUTLIER) cc_final: 0.8606 (p) REVERT: E 97 VAL cc_start: 0.7811 (OUTLIER) cc_final: 0.7336 (t) REVERT: E 140 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.7898 (mtm) REVERT: E 178 LEU cc_start: 0.8567 (tp) cc_final: 0.8336 (tp) REVERT: E 237 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8364 (mp) outliers start: 34 outliers final: 18 residues processed: 225 average time/residue: 0.2333 time to fit residues: 71.2494 Evaluate side-chains 232 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 208 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 144 ILE 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 A residue 457 CYS Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 232 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 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 237 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 37 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 103 optimal weight: 0.2980 chunk 33 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.124167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.109715 restraints weight = 13522.456| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.23 r_work: 0.3343 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8630 Z= 0.151 Angle : 0.629 11.114 11752 Z= 0.322 Chirality : 0.044 0.247 1369 Planarity : 0.004 0.066 1479 Dihedral : 5.016 55.601 1214 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.92 % Allowed : 18.32 % 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 (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: -0.05 (0.26), residues: 1102 helix: 2.14 (0.30), residues: 342 sheet: -0.36 (0.31), residues: 281 loop : -1.48 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.004 0.001 HIS B 189 PHE 0.023 0.001 PHE A 195 TYR 0.018 0.001 TYR E 190 ARG 0.003 0.000 ARG C 52 Details of bonding type rmsd hydrogen bonds : bond 0.04436 ( 395) hydrogen bonds : angle 4.72820 ( 1104) SS BOND : bond 0.00750 ( 3) SS BOND : angle 1.05051 ( 6) covalent geometry : bond 0.00341 ( 8627) covalent geometry : angle 0.62869 (11746) *********************** 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 245 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 211 time to evaluate : 1.034 Fit side-chains REVERT: A 43 LEU cc_start: 0.7657 (mt) cc_final: 0.7348 (mt) REVERT: A 393 LEU cc_start: 0.7782 (tp) cc_final: 0.7535 (tt) REVERT: A 403 TYR cc_start: 0.7592 (t80) cc_final: 0.7347 (t80) REVERT: B 218 ASP cc_start: 0.7610 (t0) cc_final: 0.7370 (t0) REVERT: B 272 LYS cc_start: 0.8834 (pttt) cc_final: 0.8548 (ttpt) REVERT: B 343 ILE cc_start: 0.8538 (mm) cc_final: 0.8299 (mt) REVERT: C 81 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7295 (mt) REVERT: C 219 ARG cc_start: 0.8289 (mmt-90) cc_final: 0.7978 (mmt-90) REVERT: C 239 ASN cc_start: 0.7930 (m-40) cc_final: 0.6653 (t0) REVERT: E 91 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8588 (p) REVERT: E 97 VAL cc_start: 0.7787 (OUTLIER) cc_final: 0.7279 (t) REVERT: E 101 TYR cc_start: 0.8065 (m-80) cc_final: 0.7636 (m-80) REVERT: E 140 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.7944 (mtm) REVERT: E 178 LEU cc_start: 0.8574 (tp) cc_final: 0.8364 (tt) REVERT: E 237 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8346 (mp) outliers start: 34 outliers final: 23 residues processed: 227 average time/residue: 0.3087 time to fit residues: 96.3360 Evaluate side-chains 236 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 208 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 144 ILE Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain B residue 5 LEU 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 232 ILE 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 64 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 140 MET 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 25 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 81 optimal weight: 20.0000 chunk 5 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.123791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.109268 restraints weight = 13547.533| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.23 r_work: 0.3337 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8630 Z= 0.165 Angle : 0.642 10.985 11752 Z= 0.327 Chirality : 0.045 0.214 1369 Planarity : 0.004 0.069 1479 Dihedral : 5.026 55.169 1214 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.26 % Allowed : 19.47 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.26), residues: 1102 helix: 2.10 (0.30), residues: 343 sheet: -0.40 (0.31), residues: 282 loop : -1.45 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 82 HIS 0.004 0.001 HIS B 189 PHE 0.021 0.002 PHE A 195 TYR 0.019 0.001 TYR E 190 ARG 0.005 0.000 ARG C 52 Details of bonding type rmsd hydrogen bonds : bond 0.04600 ( 395) hydrogen bonds : angle 4.72494 ( 1104) SS BOND : bond 0.00847 ( 3) SS BOND : angle 1.17628 ( 6) covalent geometry : bond 0.00375 ( 8627) covalent geometry : angle 0.64189 (11746) *********************** 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: 37 poor density : 208 time to evaluate : 1.371 Fit side-chains REVERT: A 393 LEU cc_start: 0.7826 (tp) cc_final: 0.7561 (tt) REVERT: A 404 ASN cc_start: 0.8939 (m110) cc_final: 0.8735 (m110) REVERT: B 218 ASP cc_start: 0.7647 (t0) cc_final: 0.7403 (t0) REVERT: B 272 LYS cc_start: 0.8839 (pttt) cc_final: 0.8571 (ttpt) REVERT: B 343 ILE cc_start: 0.8535 (mm) cc_final: 0.8296 (mt) REVERT: C 81 ILE cc_start: 0.7613 (OUTLIER) cc_final: 0.7290 (mt) REVERT: C 239 ASN cc_start: 0.7949 (m-40) cc_final: 0.6668 (t0) REVERT: C 246 ASP cc_start: 0.7800 (t70) cc_final: 0.7293 (t0) REVERT: E 91 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8622 (p) REVERT: E 97 VAL cc_start: 0.7805 (OUTLIER) cc_final: 0.7324 (t) REVERT: E 101 TYR cc_start: 0.8096 (m-80) cc_final: 0.7636 (m-80) REVERT: E 140 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.7906 (mtm) REVERT: E 178 LEU cc_start: 0.8562 (tp) cc_final: 0.8351 (tt) REVERT: E 237 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8365 (mp) outliers start: 37 outliers final: 23 residues processed: 231 average time/residue: 0.2276 time to fit residues: 71.0265 Evaluate side-chains 235 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 207 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 144 ILE Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain B residue 5 LEU 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 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 327 VAL 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 91 THR Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 174 LEU 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 91 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.123603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.109057 restraints weight = 13699.742| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.24 r_work: 0.3336 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8630 Z= 0.170 Angle : 0.646 10.883 11752 Z= 0.329 Chirality : 0.045 0.241 1369 Planarity : 0.004 0.071 1479 Dihedral : 5.117 56.928 1214 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.49 % Allowed : 20.05 % 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 (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: -0.05 (0.26), residues: 1102 helix: 2.11 (0.30), residues: 343 sheet: -0.40 (0.31), residues: 282 loop : -1.42 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 148 HIS 0.004 0.001 HIS B 196 PHE 0.020 0.002 PHE A 195 TYR 0.019 0.001 TYR E 190 ARG 0.005 0.000 ARG C 52 Details of bonding type rmsd hydrogen bonds : bond 0.04637 ( 395) hydrogen bonds : angle 4.74412 ( 1104) SS BOND : bond 0.00841 ( 3) SS BOND : angle 1.17218 ( 6) covalent geometry : bond 0.00387 ( 8627) covalent geometry : angle 0.64584 (11746) *********************** 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 251 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 212 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: A 393 LEU cc_start: 0.7821 (tp) cc_final: 0.7562 (tt) REVERT: B 23 LEU cc_start: 0.8340 (mt) cc_final: 0.8108 (mp) REVERT: B 218 ASP cc_start: 0.7646 (t0) cc_final: 0.7414 (t0) REVERT: B 272 LYS cc_start: 0.8836 (pttt) cc_final: 0.8574 (ttpt) REVERT: B 343 ILE cc_start: 0.8542 (mm) cc_final: 0.8304 (mt) REVERT: C 81 ILE cc_start: 0.7595 (OUTLIER) cc_final: 0.7294 (mt) REVERT: C 239 ASN cc_start: 0.7957 (m-40) cc_final: 0.6692 (t0) REVERT: E 91 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8611 (p) REVERT: E 97 VAL cc_start: 0.7782 (OUTLIER) cc_final: 0.7302 (t) REVERT: E 101 TYR cc_start: 0.8121 (m-80) cc_final: 0.7701 (m-80) REVERT: E 140 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.7935 (mtm) REVERT: E 178 LEU cc_start: 0.8555 (tp) cc_final: 0.8342 (tt) REVERT: E 237 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8365 (mp) outliers start: 39 outliers final: 28 residues processed: 234 average time/residue: 0.2282 time to fit residues: 72.0527 Evaluate side-chains 244 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 211 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 144 ILE 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 A residue 457 CYS 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 84 SER Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 232 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 327 VAL 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 83 MET Chi-restraints excluded: chain E residue 84 THR 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 140 MET Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 237 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 106 optimal weight: 0.0170 chunk 63 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 0.0070 chunk 82 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN C 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.125059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.110013 restraints weight = 13569.795| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.30 r_work: 0.3356 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2324 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= 0.132 Angle : 0.621 10.626 11752 Z= 0.316 Chirality : 0.044 0.234 1369 Planarity : 0.004 0.071 1479 Dihedral : 4.996 56.570 1214 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.15 % Allowed : 20.62 % 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 (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: 0.05 (0.26), residues: 1102 helix: 2.21 (0.30), residues: 343 sheet: -0.35 (0.31), residues: 282 loop : -1.38 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 148 HIS 0.004 0.001 HIS B 196 PHE 0.017 0.001 PHE A 61 TYR 0.017 0.001 TYR E 50 ARG 0.004 0.000 ARG C 52 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 395) hydrogen bonds : angle 4.63324 ( 1104) SS BOND : bond 0.00672 ( 3) SS BOND : angle 0.93539 ( 6) covalent geometry : bond 0.00292 ( 8627) covalent geometry : angle 0.62113 (11746) *********************** 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 244 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 208 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 393 LEU cc_start: 0.7759 (tp) cc_final: 0.7489 (tt) REVERT: A 450 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8348 (p) REVERT: B 23 LEU cc_start: 0.8302 (mt) cc_final: 0.8072 (mp) REVERT: B 218 ASP cc_start: 0.7602 (t0) cc_final: 0.7375 (t0) REVERT: B 272 LYS cc_start: 0.8805 (pttt) cc_final: 0.8555 (ttpt) REVERT: B 343 ILE cc_start: 0.8565 (mm) cc_final: 0.8317 (mt) REVERT: C 52 ARG cc_start: 0.7986 (ptp90) cc_final: 0.7644 (ptp90) REVERT: C 81 ILE cc_start: 0.7537 (OUTLIER) cc_final: 0.7210 (mt) REVERT: C 219 ARG cc_start: 0.8279 (mmt-90) cc_final: 0.7953 (mmt-90) REVERT: C 246 ASP cc_start: 0.7802 (t70) cc_final: 0.7338 (t0) REVERT: E 91 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8594 (p) REVERT: E 97 VAL cc_start: 0.7742 (OUTLIER) cc_final: 0.7230 (t) REVERT: E 101 TYR cc_start: 0.8049 (m-80) cc_final: 0.7607 (m-80) REVERT: E 140 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.7960 (mtm) outliers start: 36 outliers final: 23 residues processed: 227 average time/residue: 0.2076 time to fit residues: 63.6921 Evaluate side-chains 230 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 143 MET Chi-restraints excluded: chain A residue 144 ILE 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 A residue 457 CYS 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 81 ILE Chi-restraints excluded: chain C residue 84 SER 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 C residue 336 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 90 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 174 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 37 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.123005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.108385 restraints weight = 13761.469| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.26 r_work: 0.3324 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8630 Z= 0.192 Angle : 0.672 11.922 11752 Z= 0.341 Chirality : 0.046 0.242 1369 Planarity : 0.005 0.075 1479 Dihedral : 5.147 57.180 1213 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.15 % Allowed : 20.74 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.26), residues: 1102 helix: 2.10 (0.29), residues: 344 sheet: -0.35 (0.32), residues: 282 loop : -1.44 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 148 HIS 0.004 0.001 HIS B 189 PHE 0.020 0.002 PHE A 195 TYR 0.019 0.002 TYR E 190 ARG 0.004 0.000 ARG C 52 Details of bonding type rmsd hydrogen bonds : bond 0.04873 ( 395) hydrogen bonds : angle 4.80670 ( 1104) SS BOND : bond 0.00928 ( 3) SS BOND : angle 1.29066 ( 6) covalent geometry : bond 0.00441 ( 8627) covalent geometry : angle 0.67110 (11746) *********************** 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 247 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 211 time to evaluate : 1.181 Fit side-chains revert: symmetry clash REVERT: A 393 LEU cc_start: 0.7845 (tp) cc_final: 0.7589 (tt) REVERT: B 23 LEU cc_start: 0.8342 (mt) cc_final: 0.8117 (mp) REVERT: B 218 ASP cc_start: 0.7688 (t0) cc_final: 0.7439 (t0) REVERT: B 272 LYS cc_start: 0.8850 (pttt) cc_final: 0.8603 (ttpt) REVERT: B 343 ILE cc_start: 0.8538 (mm) cc_final: 0.8296 (mt) REVERT: C 81 ILE cc_start: 0.7616 (OUTLIER) cc_final: 0.7309 (mt) REVERT: E 91 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8634 (p) REVERT: E 97 VAL cc_start: 0.7810 (OUTLIER) cc_final: 0.7333 (t) REVERT: E 140 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.7946 (mtm) REVERT: E 222 GLU cc_start: 0.7283 (tm-30) cc_final: 0.7047 (tm-30) REVERT: E 237 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8385 (mp) outliers start: 36 outliers final: 26 residues processed: 233 average time/residue: 0.2238 time to fit residues: 70.9959 Evaluate side-chains 240 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 143 MET Chi-restraints excluded: chain A residue 144 ILE 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 A residue 457 CYS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 344 ILE 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 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 336 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 90 ASP 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 140 MET Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 237 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 96 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3657 r_free = 0.3657 target = 0.124094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.109484 restraints weight = 13589.503| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.25 r_work: 0.3343 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8630 Z= 0.161 Angle : 0.648 10.062 11752 Z= 0.330 Chirality : 0.045 0.248 1369 Planarity : 0.004 0.076 1479 Dihedral : 5.098 57.806 1213 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.69 % Allowed : 21.54 % 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 (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: -0.03 (0.26), residues: 1102 helix: 2.10 (0.29), residues: 347 sheet: -0.34 (0.31), residues: 281 loop : -1.46 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 148 HIS 0.004 0.001 HIS B 196 PHE 0.018 0.001 PHE A 195 TYR 0.018 0.001 TYR E 190 ARG 0.006 0.000 ARG C 52 Details of bonding type rmsd hydrogen bonds : bond 0.04533 ( 395) hydrogen bonds : angle 4.71520 ( 1104) SS BOND : bond 0.00802 ( 3) SS BOND : angle 1.12718 ( 6) covalent geometry : bond 0.00367 ( 8627) covalent geometry : angle 0.64797 (11746) ********************** 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 242 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: A 72 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8524 (tt) REVERT: A 393 LEU cc_start: 0.7820 (tp) cc_final: 0.7556 (tt) REVERT: A 450 THR cc_start: 0.8542 (OUTLIER) cc_final: 0.8310 (p) REVERT: B 23 LEU cc_start: 0.8317 (mt) cc_final: 0.8076 (mp) REVERT: B 218 ASP cc_start: 0.7667 (t0) cc_final: 0.7425 (t0) REVERT: B 272 LYS cc_start: 0.8828 (pttt) cc_final: 0.8583 (ttpt) REVERT: B 343 ILE cc_start: 0.8535 (mm) cc_final: 0.8293 (mt) REVERT: C 81 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.7262 (mt) REVERT: C 219 ARG cc_start: 0.8252 (mmt-90) cc_final: 0.7946 (mmt-90) REVERT: C 246 ASP cc_start: 0.7819 (t70) cc_final: 0.7364 (t0) REVERT: E 91 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8612 (p) REVERT: E 97 VAL cc_start: 0.7749 (OUTLIER) cc_final: 0.7264 (t) REVERT: E 101 TYR cc_start: 0.8111 (m-80) cc_final: 0.7688 (m-80) REVERT: E 140 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.7932 (mtm) REVERT: E 237 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8366 (mp) outliers start: 32 outliers final: 21 residues processed: 228 average time/residue: 0.2201 time to fit residues: 67.4814 Evaluate side-chains 236 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 208 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 143 MET Chi-restraints excluded: chain A residue 144 ILE 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 A residue 457 CYS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 344 ILE 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 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 336 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 90 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 237 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 58 optimal weight: 0.3980 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 0.0070 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.125296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.110588 restraints weight = 13849.631| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.29 r_work: 0.3349 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2460 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= 0.136 Angle : 0.641 10.115 11752 Z= 0.322 Chirality : 0.044 0.236 1369 Planarity : 0.004 0.075 1479 Dihedral : 5.133 65.056 1213 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.46 % Allowed : 21.66 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.26), residues: 1102 helix: 2.22 (0.29), residues: 346 sheet: -0.40 (0.31), residues: 284 loop : -1.44 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 148 HIS 0.004 0.001 HIS B 196 PHE 0.018 0.001 PHE A 61 TYR 0.017 0.001 TYR E 190 ARG 0.006 0.000 ARG C 52 Details of bonding type rmsd hydrogen bonds : bond 0.04220 ( 395) hydrogen bonds : angle 4.62557 ( 1104) SS BOND : bond 0.00690 ( 3) SS BOND : angle 0.91861 ( 6) covalent geometry : bond 0.00305 ( 8627) covalent geometry : angle 0.64121 (11746) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5357.53 seconds wall clock time: 94 minutes 33.37 seconds (5673.37 seconds total)